gmxpreprocess: clean up -Wunused-parameter warnings

Clean up (most) of unused params

Change-Id: I1805a829682baf54047390442bfcfa2a95cd0ee1
Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>

diff --git a/src/gromacs/gmxpreprocess/gen_vsite.c b/src/gromacs/gmxpreprocess/gen_vsite.c
index 36650dec77ef9bfabbdf2b6c301eb31fa0b65740..a8d5ea9d1fbe502245592806d8ac1bcffe9d0345 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_vsite.c
+++ b/src/gromacs/gmxpreprocess/gen_vsite.c
@@ -683,7 +683,7 @@ static void add_vsites(t_params plist[], int vsite_type[],
 
 static int gen_vsites_6ring(t_atoms *at, int *vsite_type[], t_params plist[],
                             int nrfound, int *ats, real bond_cc, real bond_ch,
-                            real xcom, real ycom, gmx_bool bDoZ)
+                            real xcom, gmx_bool bDoZ)
 {
     /* these MUST correspond to the atnms array in do_vsite_aromatics! */
     enum {
@@ -781,7 +781,7 @@ static int gen_vsites_phe(t_atoms *at, int *vsite_type[], t_params plist[],
                           int nrfound, int *ats, t_vsitetop *vsitetop, int nvsitetop)
 {
     real bond_cc, bond_ch;
-    real xcom, ycom, mtot;
+    real xcom, mtot;
     int  i;
     /* these MUST correspond to the atnms array in do_vsite_aromatics! */
     enum {
@@ -818,17 +818,15 @@ static int gen_vsites_phe(t_atoms *at, int *vsite_type[], t_params plist[],
     x[atHZ]  = x[atCZ]+bond_ch;
     y[atHZ]  = 0;
 
-    xcom = ycom = mtot = 0;
+    xcom = mtot = 0;
     for (i = 0; i < atNR; i++)
     {
         xcom += x[i]*at->atom[ats[i]].m;
-        ycom += y[i]*at->atom[ats[i]].m;
         mtot += at->atom[ats[i]].m;
     }
     xcom /= mtot;
-    ycom /= mtot;
 
-    return gen_vsites_6ring(at, vsite_type, plist, nrfound, ats, bond_cc, bond_ch, xcom, ycom, TRUE);
+    return gen_vsites_6ring(at, vsite_type, plist, nrfound, ats, bond_cc, bond_ch, xcom, TRUE);
 }
 
 static void calc_vsite3_param(real xd, real yd, real xi, real yi, real xj, real yj,
@@ -1139,7 +1137,7 @@ static int gen_vsites_tyr(gpp_atomtype_t atype, rvec *newx[],
     int  nvsite, i, i0, j, atM, tpM;
     real dCGCE, dCEOH, dCGM, tmp1, a, b;
     real bond_cc, bond_ch, bond_co, bond_oh, angle_coh;
-    real xcom, ycom, mtot;
+    real xcom, mtot;
     real vmass, vdist, mM;
     rvec r1;
     char name[10];
@@ -1190,19 +1188,17 @@ static int gen_vsites_tyr(gpp_atomtype_t atype, rvec *newx[],
     xi[atOH]  = xi[atCZ]+bond_co;
     yi[atOH]  = 0;
 
-    xcom = ycom = mtot = 0;
+    xcom = mtot = 0;
     for (i = 0; i < atOH; i++)
     {
         xcom += xi[i]*at->atom[ats[i]].m;
-        ycom += yi[i]*at->atom[ats[i]].m;
         mtot += at->atom[ats[i]].m;
     }
     xcom /= mtot;
-    ycom /= mtot;
 
     /* first do 6 ring as default,
        except CZ (we'll do that different) and HZ (we don't have that): */
-    nvsite = gen_vsites_6ring(at, vsite_type, plist, nrfound, ats, bond_cc, bond_ch, xcom, ycom, FALSE);
+    nvsite = gen_vsites_6ring(at, vsite_type, plist, nrfound, ats, bond_cc, bond_ch, xcom, FALSE);
 
     /* then construct CZ from the 2nd triangle */
     /* vsite3 construction: r_d = r_i + a r_ij + b r_ik */

diff --git a/src/gromacs/gmxpreprocess/pdb2top.c b/src/gromacs/gmxpreprocess/pdb2top.c
index a094258434b213b578094d969bf1e3af7c9cda28..0237afc893e333396856289de1dbe6b93635103b 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2top.c
+++ b/src/gromacs/gmxpreprocess/pdb2top.c
@@ -770,8 +770,7 @@ static void do_ssbonds(t_params *ps, t_atoms *atoms,
 static void at2bonds(t_params *psb, t_hackblock *hb,
                      t_atoms *atoms,
                      rvec x[],
-                     real long_bond_dist, real short_bond_dist,
-                     gmx_bool bAllowMissing)
+                     real long_bond_dist, real short_bond_dist)
 {
     int         resind, i, j, k;
     atom_id     ai, aj;
@@ -967,7 +966,7 @@ static void check_restp_types(t_restp *r0, t_restp *r1)
     }
 }
 
-void add_atom_to_restp(t_restp *restp, int resnr, int at_start, const t_hack *hack)
+void add_atom_to_restp(t_restp *restp, int at_start, const t_hack *hack)
 {
     char        buf[STRLEN];
     int         k;
@@ -1149,8 +1148,7 @@ void get_hackblocks_rtp(t_hackblock **hb, t_restp **restp,
                     if ( (*hb)[i].hack[j].oname == NULL)
                     {
                         /* we're adding: */
-                        add_atom_to_restp(&(*restp)[i], resinfo[i].nr, l,
-                                          &(*hb)[i].hack[j]);
+                        add_atom_to_restp(&(*restp)[i], l, &(*hb)[i].hack[j]);
                     }
                     else
                     {
@@ -1322,8 +1320,7 @@ static gmx_bool match_atomnames_with_rtp_atom(t_atoms *pdba, rvec *x, int atind,
                                       start_at, rptr->resname, newnm);
                         }
                         /* We can add the atom after atom start_nr */
-                        add_atom_to_restp(rptr, resnr, start_nr,
-                                          &hbr->hack[j]);
+                        add_atom_to_restp(rptr, start_nr, &hbr->hack[j]);
 
                         bFoundInAdd = TRUE;
                     }
@@ -1524,10 +1521,9 @@ void pdb2top(FILE *top_file, char *posre_fn, char *molname,
              t_atoms *atoms, rvec **x, gpp_atomtype_t atype, t_symtab *tab,
              int nrtp, t_restp rtp[],
              t_restp *restp, t_hackblock *hb,
-             int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
              gmx_bool bAllowMissing,
              gmx_bool bVsites, gmx_bool bVsiteAromatics,
-             const char *ff, const char *ffdir,
+             const char *ffdir,
              real mHmult,
              int nssbonds, t_ssbond *ssbonds,
              real long_bond_dist, real short_bond_dist,
@@ -1559,7 +1555,7 @@ void pdb2top(FILE *top_file, char *posre_fn, char *molname,
     /* Make bonds */
     at2bonds(&(plist[F_BONDS]), hb,
              atoms, *x,
-             long_bond_dist, short_bond_dist, bAllowMissing);
+             long_bond_dist, short_bond_dist);
 
     /* specbonds: disulphide bonds & heme-his */
     do_ssbonds(&(plist[F_BONDS]),

diff --git a/src/gromacs/gmxpreprocess/readir.c b/src/gromacs/gmxpreprocess/readir.c
index 641e7dc5a160fc8eff8bb481936afe591ab1719a..bc8a72ab64c0a93417b460289ef077644678dd72 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.c
+++ b/src/gromacs/gmxpreprocess/readir.c
@@ -2733,7 +2733,7 @@ static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
     sfree(na_vcm);
 }
 
-static void decode_cos(char *s, t_cosines *cosine, gmx_bool bTime)
+static void decode_cos(char *s, t_cosines *cosine)
 {
     char   *t;
     char    format[STRLEN], f1[STRLEN];
@@ -3385,12 +3385,12 @@ void do_index(const char* mdparin, const char *ndx,
         gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
     }
 
-    decode_cos(efield_x, &(ir->ex[XX]), FALSE);
-    decode_cos(efield_xt, &(ir->et[XX]), TRUE);
-    decode_cos(efield_y, &(ir->ex[YY]), FALSE);
-    decode_cos(efield_yt, &(ir->et[YY]), TRUE);
-    decode_cos(efield_z, &(ir->ex[ZZ]), FALSE);
-    decode_cos(efield_zt, &(ir->et[ZZ]), TRUE);
+    decode_cos(efield_x, &(ir->ex[XX]));
+    decode_cos(efield_xt, &(ir->et[XX]));
+    decode_cos(efield_y, &(ir->ex[YY]));
+    decode_cos(efield_yt, &(ir->et[YY]));
+    decode_cos(efield_z, &(ir->ex[ZZ]));
+    decode_cos(efield_zt, &(ir->et[ZZ]));
 
     if (ir->bAdress)
     {

diff --git a/src/gromacs/gmxpreprocess/readir.h b/src/gromacs/gmxpreprocess/readir.h
index 0fbcde0ae826f43c1178b8bf9ff9b34d45b8ed73..4bf1c5334fba8057e92f49f0d595ebd5d43a7577 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.h
+++ b/src/gromacs/gmxpreprocess/readir.h
@@ -154,7 +154,7 @@ extern void make_rotation_groups(t_rot *rot, char **rotgnames,
                                  t_blocka *grps, char **gnames);
 /* Process the rotation parameters after reading the index groups */
 
-extern void set_reference_positions(t_rot *rot, gmx_mtop_t *mtop, rvec *x, matrix box,
+extern void set_reference_positions(t_rot *rot, rvec *x, matrix box,
                                     const char *fn, gmx_bool bSet, warninp_t wi);
 
 #endif  /* _readir_h */

diff --git a/src/gromacs/gmxpreprocess/readrot.c b/src/gromacs/gmxpreprocess/readrot.c
index 4a070f2824e9c55707e7bb078091df719dc019f1..ca05f8c3eb796b72b87f4cf280a90711d31d794e 100644 (file)
--- a/src/gromacs/gmxpreprocess/readrot.c
+++ b/src/gromacs/gmxpreprocess/readrot.c
@@ -232,7 +232,7 @@ static void check_box_unchanged(matrix f_box, matrix box, char fn[], warninp_t w
 
 /* Extract the reference positions for the rotation group(s) */
 extern void set_reference_positions(
-        t_rot *rot, gmx_mtop_t *mtop, rvec *x, matrix box,
+        t_rot *rot, rvec *x, matrix box,
         const char *fn, gmx_bool bSet, warninp_t wi)
 {
     int         g, i, ii;

diff --git a/src/gromacs/gmxpreprocess/ter_db.c b/src/gromacs/gmxpreprocess/ter_db.c
index 93a9cf441f8b8f8cecc6eab72a0a84f27e68db76..88ec7168f98c54125243c474421068a38aafcd0e 100644 (file)
--- a/src/gromacs/gmxpreprocess/ter_db.c
+++ b/src/gromacs/gmxpreprocess/ter_db.c
@@ -139,7 +139,7 @@ static void read_atom(char *line, gmx_bool bAdd,
     }
 }
 
-static void print_atom(FILE *out, t_atom *a, gpp_atomtype_t atype, char *newnm)
+static void print_atom(FILE *out, t_atom *a, gpp_atomtype_t atype)
 {
     fprintf(out, "\t%s\t%g\t%g\n",
             get_atomtype_name(a->type, atype), a->m, a->q);
@@ -190,7 +190,7 @@ static void print_ter_db(const char *ff, char C, int nb, t_hackblock tb[],
                 if (tb[i].hack[j].oname != NULL && tb[i].hack[j].nname != NULL)
                 {
                     fprintf(out, "%s\t", tb[i].hack[j].oname);
-                    print_atom(out, tb[i].hack[j].atom, atype, tb[i].hack[j].nname);
+                    print_atom(out, tb[i].hack[j].atom, atype);
                 }
             }
         }
@@ -202,7 +202,7 @@ static void print_ter_db(const char *ff, char C, int nb, t_hackblock tb[],
                 if (tb[i].hack[j].oname == NULL && tb[i].hack[j].nname != NULL)
                 {
                     print_ab(out, &(tb[i].hack[j]), tb[i].hack[j].nname);
-                    print_atom(out, tb[i].hack[j].atom, atype, tb[i].hack[j].nname);
+                    print_atom(out, tb[i].hack[j].atom, atype);
                 }
             }
         }

diff --git a/src/gromacs/gmxpreprocess/topio.c b/src/gromacs/gmxpreprocess/topio.c
index 09581bb6af476e7db733f75edb8c754e08d576d0..9023b513be09b67ca562084de93e299af5c6a9e4 100644 (file)
--- a/src/gromacs/gmxpreprocess/topio.c
+++ b/src/gromacs/gmxpreprocess/topio.c
@@ -119,7 +119,7 @@ static int copy_nbparams(t_nbparam **param, int ftype, t_params *plist, int nr)
     return ncopy;
 }
 
-static void gen_pairs(t_params *nbs, t_params *pairs, real fudge, int comb, gmx_bool bVerbose)
+static void gen_pairs(t_params *nbs, t_params *pairs, real fudge, int comb)
 {
     int     i, j, ntp, nrfp, nrfpA, nrfpB, nnn;
     real    scaling;
@@ -294,7 +294,6 @@ static void get_nbparm(char *nb_str, char *comb_str, int *nb, int *comb,
 }
 
 static char ** cpp_opts(const char *define, const char *include,
-                        const char *infile,
                         warninp_t wi)
 {
     int         n, len;
@@ -550,7 +549,6 @@ static char **read_topol(const char *infile, const char *outfile,
                          gmx_bool        bFEP,
                          gmx_bool        bGenborn,
                          gmx_bool        bZero,
-                         gmx_bool        bVerbose,
                          warninp_t   wi)
 {
     FILE           *out;
@@ -596,7 +594,7 @@ static char **read_topol(const char *infile, const char *outfile,
     }
 
     /* open input file */
-    status = cpp_open_file(infile, &handle, cpp_opts(define, include, infile, wi));
+    status = cpp_open_file(infile, &handle, cpp_opts(define, include, wi));
     if (status != 0)
     {
         gmx_fatal(FARGS, cpp_error(&handle, status));
@@ -869,7 +867,7 @@ static char **read_topol(const char *infile, const char *outfile,
                                 free_nbparam(nbparam, ntype);
                                 if (bGenPairs)
                                 {
-                                    gen_pairs(&(plist[nb_funct]), &(plist[F_LJ14]), fudgeLJ, comb, bVerbose);
+                                    gen_pairs(&(plist[nb_funct]), &(plist[F_LJ14]), fudgeLJ, comb);
                                     ncopy = copy_nbparams(pair, nb_funct, &(plist[F_LJ14]),
                                                           ntype);
                                     fprintf(stderr, "Generated %d of the %d 1-4 parameter combinations\n", ncombs-ncopy, ncombs);
@@ -916,12 +914,11 @@ static char **read_topol(const char *infile, const char *outfile,
                                       bGenPairs, *fudgeQQ, bZero, &bWarn_copy_A_B, wi);
                             break;
                         case d_cmap:
-                            push_cmap(d, plist, mi0->plist, &(mi0->atoms), atype, pline,
-                                      &bWarn_copy_A_B, wi);
+                            push_cmap(d, plist, mi0->plist, &(mi0->atoms), atype, pline,wi);
                             break;
 
                         case d_vsitesn:
-                            push_vsitesn(d, plist, mi0->plist, &(mi0->atoms), atype, pline, wi);
+                            push_vsitesn(d, plist, &(mi0->atoms), pline, wi);
                             break;
                         case d_exclusions:
                             assert(block2);
@@ -974,7 +971,7 @@ static char **read_topol(const char *infile, const char *outfile,
                                               &(mi0->excls));
                                 merge_excl(&(mi0->excls), &(block2[whichmol]));
                                 done_block2(&(block2[whichmol]));
-                                make_shake(mi0->plist, &mi0->atoms, atype, opts->nshake);
+                                make_shake(mi0->plist, &mi0->atoms, opts->nshake);
 
 
 
@@ -1104,8 +1101,7 @@ char **do_top(gmx_bool          bVerbose,
                        symtab, atype, nrmols, molinfo,
                        plist, combination_rule, repulsion_power,
                        opts, fudgeQQ, nmolblock, molblock,
-                       ir->efep != efepNO, bGenborn, bZero, bVerbose,
-                       wi);
+                       ir->efep != efepNO, bGenborn, bZero, wi);
     if ((*combination_rule != eCOMB_GEOMETRIC) &&
         (ir->vdwtype == evdwUSER))
     {

diff --git a/src/gromacs/gmxpreprocess/toppush.c b/src/gromacs/gmxpreprocess/toppush.c
index f5cdad1f29d24924611474fef21cb3404967b522..95523b00da2bedc1c8f279121219e7e325e0c589 100644 (file)
--- a/src/gromacs/gmxpreprocess/toppush.c
+++ b/src/gromacs/gmxpreprocess/toppush.c
@@ -1209,7 +1209,7 @@ push_cmaptype(directive d, t_params bt[], int nral, gpp_atomtype_t at,
 static void push_atom_now(t_symtab *symtab, t_atoms *at, int atomnr,
                           int atomicnumber,
                           int type, char *ctype, int ptype,
-                          char *resnumberic, int cgnumber,
+                          char *resnumberic,
                           char *resname, char *name, real m0, real q0,
                           int typeB, char *ctypeB, real mB, real qB)
 {
@@ -1384,7 +1384,7 @@ void push_atom(t_symtab *symtab, t_block *cgs,
     push_cg(cgs, lastcg, cgnumber, nr);
 
     push_atom_now(symtab, at, atomnr, get_atomtype_atomnumber(type, atype),
-                  type, ctype, ptype, resnumberic, cgnumber,
+                  type, ctype, ptype, resnumberic,
                   resname, name, m0, q0, typeB,
                   typeB == type ? ctype : ctypeB, mB, qB);
 }
@@ -1517,7 +1517,7 @@ static gmx_bool default_nb_params(int ftype, t_params bt[], t_atoms *at,
     return bFound;
 }
 
-static gmx_bool default_cmap_params(int ftype, t_params bondtype[],
+static gmx_bool default_cmap_params(t_params bondtype[],
                                     t_atoms *at, gpp_atomtype_t atype,
                                     t_param *p, gmx_bool bB,
                                     int *cmap_type, int *nparam_def)
@@ -2080,7 +2080,6 @@ void push_bond(directive d, t_params bondtype[], t_params bond[],
 
 void push_cmap(directive d, t_params bondtype[], t_params bond[],
                t_atoms *at, gpp_atomtype_t atype, char *line,
-               gmx_bool *bWarn_copy_A_B,
                warninp_t wi)
 {
     const char *aaformat[MAXATOMLIST+1] =
@@ -2154,7 +2153,7 @@ void push_cmap(directive d, t_params bondtype[], t_params bond[],
     }
 
     /* Get the cmap type for this cmap angle */
-    bFound = default_cmap_params(ftype, bondtype, at, atype, &param, FALSE, &cmap_type, &ncmap_params);
+    bFound = default_cmap_params(bondtype, at, atype, &param, FALSE, &cmap_type, &ncmap_params);
 
     /* We want exactly one parameter (the cmap type in state A (currently no state B) back */
     if (bFound && ncmap_params == 1)
@@ -2173,8 +2172,8 @@ void push_cmap(directive d, t_params bondtype[], t_params bond[],
 
 
 
-void push_vsitesn(directive d, t_params bondtype[], t_params bond[],
-                  t_atoms *at, gpp_atomtype_t atype, char *line,
+void push_vsitesn(directive d, t_params bond[],
+                  t_atoms *at, char *line,
                   warninp_t wi)
 {
     char   *ptr;

diff --git a/src/gromacs/gmxpreprocess/toppush.h b/src/gromacs/gmxpreprocess/toppush.h
index cec3fcce5958449f1ab2c53949ae13529398b5e3..c5851d3d31e10d8b7c041fe72cf374c22ccd296f 100644 (file)
--- a/src/gromacs/gmxpreprocess/toppush.h
+++ b/src/gromacs/gmxpreprocess/toppush.h
@@ -96,11 +96,10 @@ extern void push_bond(directive d, t_params bondtype[], t_params bond[],
 
 extern void push_cmap(directive d, t_params bondtype[], t_params bond[],
                       t_atoms *at, gpp_atomtype_t atype, char *line,
-                      gmx_bool *bWarn_copy_A_B,
                       warninp_t wi);
 
-extern void push_vsitesn(directive d, t_params bondtype[], t_params bond[],
-                         t_atoms *at, gpp_atomtype_t atype, char *line,
+extern void push_vsitesn(directive d, t_params bond[],
+                         t_atoms *at, char *line,
                          warninp_t wi);
 
 extern void push_mol(int nrmols, t_molinfo mols[], char *pline,

diff --git a/src/gromacs/gmxpreprocess/topshake.c b/src/gromacs/gmxpreprocess/topshake.c
index ff511e37ef62ee081d7d5419f469100ff0ade724..f378850b3e684ba2e6d6ec12ee476092c5766db5 100644 (file)
--- a/src/gromacs/gmxpreprocess/topshake.c
+++ b/src/gromacs/gmxpreprocess/topshake.c
@@ -101,7 +101,7 @@ static int count_hydrogens (char ***atomname, int nra, atom_id a[])
     return nh;
 }
 
-void make_shake (t_params plist[], t_atoms *atoms, gpp_atomtype_t at, int nshake)
+void make_shake (t_params plist[], t_atoms *atoms, int nshake)
 {
     char          ***info = atoms->atomname;
     t_params        *pr;

diff --git a/src/gromacs/gmxpreprocess/topshake.h b/src/gromacs/gmxpreprocess/topshake.h
index 42809a20be12b2f4198eeddcdef80fc336524c8d..6e7db7522c2e569a6c444160d63c498103215c05 100644 (file)
--- a/src/gromacs/gmxpreprocess/topshake.h
+++ b/src/gromacs/gmxpreprocess/topshake.h
@@ -38,6 +38,6 @@
 
 #include "topio.h"
 
-void make_shake (t_params plist[], t_atoms *atoms, gpp_atomtype_t at, int nshake);
+void make_shake (t_params plist[], t_atoms *atoms, int nshake);
 
 #endif  /* _topshake_h */

diff --git a/src/gromacs/gmxpreprocess/vsite_parm.c b/src/gromacs/gmxpreprocess/vsite_parm.c
index 0ca77b1d8bcdd7ca5da35f7d96f7caec4530466a..678b3b0876bb5fcf0ff295b2262b9b1a476f7bab 100644 (file)
--- a/src/gromacs/gmxpreprocess/vsite_parm.c
+++ b/src/gromacs/gmxpreprocess/vsite_parm.c
@@ -110,7 +110,7 @@ static void enter_bonded(int nratoms, int *nrbonded, t_mybonded **bondeds,
 }
 
 static void get_bondeds(int nrat, t_iatom atoms[],
-                        at2vsitebond_t *at2vb, t_params plist[],
+                        at2vsitebond_t *at2vb,
                         int *nrbond, t_mybonded **bonds,
                         int *nrang,  t_mybonded **angles,
                         int *nridih, t_mybonded **idihs )
@@ -861,7 +861,7 @@ int set_vsites(gmx_bool bVerbose, t_atoms *atoms, gpp_atomtype_t atype,
                     idihs  = NULL;
                     nrset++;
                     /* now set the vsite parameters: */
-                    get_bondeds(NRAL(ftype), plist[ftype].param[i].a, at2vb, plist,
+                    get_bondeds(NRAL(ftype), plist[ftype].param[i].a, at2vb,
                                 &nrbond, &bonds, &nrang,  &angles, &nridih, &idihs);
                     if (debug)
                     {

diff --git a/src/gromacs/legacyheaders/pdb2top.h b/src/gromacs/legacyheaders/pdb2top.h
index 311b04aff98bfe301664cc3070dc7b714f74d918..16bc1b4137fab4aa55f2c8a98d23fa2dd3b0d3f6 100644 (file)
--- a/src/gromacs/legacyheaders/pdb2top.h
+++ b/src/gromacs/legacyheaders/pdb2top.h
@@ -108,10 +108,9 @@ void pdb2top(FILE *top_file, char *posre_fn, char *molname,
              gpp_atomtype_t atype, t_symtab *tab,
              int nrtp, t_restp rtp[],
              t_restp *restp, t_hackblock *hb,
-             int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
              gmx_bool bAllowMissing,
              gmx_bool bVsites, gmx_bool bVsiteAromatics,
-             const char *ff, const char *ffdir,
+             const char *ffdir,
              real mHmult,
              int nssbonds, t_ssbond ssbonds[],
              real long_bond_dist, real short_bond_dist,

diff --git a/src/programs/gmx/g_x2top.c b/src/programs/gmx/g_x2top.c
index 8a5c3d90556d1a817b5ef1c9f354922124cdd5e8..e9db6949b3d54c8202bccef2dc494b9c728b6785 100644 (file)
--- a/src/programs/gmx/g_x2top.c
+++ b/src/programs/gmx/g_x2top.c
@@ -114,8 +114,8 @@ static int get_atype(char *nm)
 }
 
 void mk_bonds(int nnm, t_nm2type nmt[],
-              t_atoms *atoms, rvec x[], t_params *bond, int nbond[], char *ff,
-              gmx_bool bPBC, matrix box, gmx_atomprop_t aps)
+              t_atoms *atoms, rvec x[], t_params *bond, int nbond[],
+              gmx_bool bPBC, matrix box)
 {
     t_param b;
     int     i, j;
@@ -374,8 +374,7 @@ static void print_pl(FILE *fp, t_params plist[], int ftp, const char *name,
 }
 
 static void print_rtp(const char *filenm, const char *title, t_atoms *atoms,
-                      t_params plist[], gpp_atomtype_t atype, int cgnr[],
-                      int nbts, int bts[])
+                      t_params plist[], gpp_atomtype_t atype, int cgnr[])
 {
     FILE *fp;
     int   i, tp;
@@ -443,7 +442,6 @@ int gmx_x2top(int argc, char *argv[])
     t_nextnb           nnb;
     t_nm2type         *nm2t;
     t_mols             mymol;
-    gmx_atomprop_t     aps;
     int                nnm;
     char               title[STRLEN], forcefield[32], ffdir[STRLEN];
     rvec              *x; /* coordinates? */
@@ -526,8 +524,6 @@ int gmx_x2top(int argc, char *argv[])
         gmx_fatal(FARGS, "Specify at least one output file");
     }
 
-    aps = gmx_atomprop_init();
-
     /* Force field selection, interactive or direct */
     choose_ff(strcmp(ff, "select") == 0 ? NULL : ff,
               forcefield, sizeof(forcefield),
@@ -569,8 +565,7 @@ int gmx_x2top(int argc, char *argv[])
     }
     printf("Generating bonds from distances...\n");
     snew(nbonds, atoms->nr);
-    mk_bonds(nnm, nm2t, atoms, x, &(plist[F_BONDS]), nbonds, forcefield,
-             bPBC, box, aps);
+    mk_bonds(nnm, nm2t, atoms, x, &(plist[F_BONDS]), nbonds, bPBC, box);
 
     open_symtab(&symtab);
     atype = set_atom_type(&symtab, atoms, &(plist[F_BONDS]), nbonds, nnm, nm2t);
@@ -623,7 +618,7 @@ int gmx_x2top(int argc, char *argv[])
     if (bRTP)
     {
         print_rtp(ftp2fn(efRTP, NFILE, fnm), "Generated by x2top",
-                  atoms, plist, atype, cgnr, asize(bts), bts);
+                  atoms, plist, atype, cgnr);
     }
 
     if (debug)

diff --git a/src/programs/gmx/grompp.c b/src/programs/gmx/grompp.c
index 6f213682171bdbe0d20adb72f0da89bed1ed456b..54bbb7904beafa11dc6069108771410d902724a4 100644 (file)
--- a/src/programs/gmx/grompp.c
+++ b/src/programs/gmx/grompp.c
@@ -1876,7 +1876,7 @@ int gmx_grompp(int argc, char *argv[])
 
     if (ir->bRot)
     {
-        set_reference_positions(ir->rot, sys, state.x, state.box,
+        set_reference_positions(ir->rot, state.x, state.box,
                                 opt2fn("-ref", NFILE, fnm), opt2bSet("-ref", NFILE, fnm),
                                 wi);
     }

diff --git a/src/programs/gmx/pdb2gmx.c b/src/programs/gmx/pdb2gmx.c
index 52d543b813e7c30e8bfe2bfbf2ff5e3a6668a1b6..c3fa5e7a8fc4eaee9a7dab704e23d4574af391b9 100644 (file)
--- a/src/programs/gmx/pdb2gmx.c
+++ b/src/programs/gmx/pdb2gmx.c
@@ -2094,8 +2094,8 @@ int gmx_pdb2gmx(int argc, char *argv[])
         pdb2top(top_file2, posre_fn, molname, pdba, &x, atype, &symtab,
                 nrtp, restp,
                 restp_chain, hb_chain,
-                cc->nterpairs, cc->ntdb, cc->ctdb, bAllowMissing,
-                bVsites, bVsiteAromatics, forcefield, ffdir,
+                bAllowMissing,
+                bVsites, bVsiteAromatics, ffdir,
                 mHmult, nssbonds, ssbonds,
                 long_bond_dist, short_bond_dist, bDeuterate, bChargeGroups, bCmap,
                 bRenumRes, bRTPresname);