Merge "Updated source for Van der Waals radii."

diff --git a/share/top/vdwradii.dat b/share/top/vdwradii.dat
index d8c1ddbd327dfc37458f3e16cb9fa5b88fba01ec..1aef7329ca1cf088c7bd874726b26aaa40a7e2bc 100644 (file)
--- a/share/top/vdwradii.dat
+++ b/share/top/vdwradii.dat
@@ -3,12 +3,17 @@
 ; longest matches are used
 ; '???' or '*' matches any residue name
 ; 'AAA' matches any protein residue name
-???  C     0.15
-???  F     0.12
-???  H     0.04
-???  N     0.110
-???  O     0.105
-???  S     0.16
+; Source: http://en.wikipedia.org/wiki/Van_der_Waals_radius
+; These come from A. Bondi, "van der Waals Volumes and Radii",
+; J. Phys. Chem. 68 (1964) 441-451
+???  H     0.12
+???  C     0.17
+???  N     0.155
+???  O     0.152
+???  F     0.147
+???  P     0.18
+???  S     0.18
+???  Cl    0.175
 ; Water charge sites
 SOL  MW    0
 SOL  LP    0

diff --git a/src/gromacs/gmxana/gmx_genbox.cpp b/src/gromacs/gmxana/gmx_genbox.cpp
index 2dc75e4f49fee386a9b6a5567d7bb6df66419a9e..2f7e68518b75c8cc2c4505522af15da9b7f7f9ab 100644 (file)
--- a/src/gromacs/gmxana/gmx_genbox.cpp
+++ b/src/gromacs/gmxana/gmx_genbox.cpp
@@ -103,7 +103,7 @@ static gmx_bool in_box(t_pbc *pbc, rvec x)
 }
 
 static void mk_vdw(t_atoms *a, real rvdw[], gmx_atomprop_t aps,
-                   real r_distance)
+                   real r_distance,real r_scale)
 {
     int i;
 
@@ -117,6 +117,10 @@ static void mk_vdw(t_atoms *a, real rvdw[], gmx_atomprop_t aps,
         {
             rvdw[i] = r_distance;
         }
+        else 
+        {
+            rvdw[i] *= r_scale;
+        }
     }
 }
 
@@ -379,7 +383,8 @@ enum {
 
 static char *insert_mols(const char *mol_insrt, int nmol_insrt, int ntry, int seed,
                          t_atoms *atoms, rvec **x, real **r, int ePBC, matrix box,
-                         gmx_atomprop_t aps, real r_distance, real rshell,
+                         gmx_atomprop_t aps, 
+                         real r_distance, real r_scale, real rshell,
                          const output_env_t oenv,
                          const char* posfn, const rvec deltaR, int enum_rot,
                          gmx_bool bCheckAllPairDist)
@@ -424,7 +429,7 @@ static char *insert_mols(const char *mol_insrt, int nmol_insrt, int ntry, int se
     srenew(atoms_insrt.resinfo, atoms_insrt.nres);
 
     /* initialise van der waals arrays of insert molecules */
-    mk_vdw(&atoms_insrt, r_insrt, aps, r_distance);
+    mk_vdw(&atoms_insrt, r_insrt, aps, r_distance, r_scale);
 
     /* With -ip, take nmol_insrt from file posfn */
     if (posfn != NULL)
@@ -532,7 +537,8 @@ static char *insert_mols(const char *mol_insrt, int nmol_insrt, int ntry, int se
 
 static void add_solv(const char *fn, t_atoms *atoms, rvec **x, rvec **v, real **r,
                      int ePBC, matrix box,
-                     gmx_atomprop_t aps, real r_distance, int *atoms_added,
+                     gmx_atomprop_t aps, 
+                     real r_distance, real r_scale, int *atoms_added,
                      int *residues_added, real rshell, int max_sol,
                      const output_env_t oenv)
 {
@@ -580,7 +586,7 @@ static void add_solv(const char *fn, t_atoms *atoms, rvec **x, rvec **v, real **
     rm_res_pbc(atoms_solvt, x_solvt, box_solvt);
 
     /* initialise van der waals arrays of solvent configuration */
-    mk_vdw(atoms_solvt, r_solvt, aps, r_distance);
+    mk_vdw(atoms_solvt, r_solvt, aps, r_distance, r_scale);
 
     /* calculate the box multiplication factors n_box[0...DIM] */
     nmol = 1;
@@ -637,7 +643,7 @@ static void add_solv(const char *fn, t_atoms *atoms, rvec **x, rvec **v, real **
 
 static char *read_prot(const char *confin, t_atoms *atoms, rvec **x, rvec **v,
                        real **r, int *ePBC, matrix box, gmx_atomprop_t aps,
-                       real r_distance)
+                       real r_distance, real r_scale)
 {
     char *title;
     int   natoms;
@@ -661,7 +667,7 @@ static char *read_prot(const char *confin, t_atoms *atoms, rvec **x, rvec **v,
             title, atoms->nr, atoms->nres);
 
     /* initialise van der waals arrays of configuration 1 */
-    mk_vdw(atoms, *r, aps, r_distance);
+    mk_vdw(atoms, *r, aps, r_distance, r_scale);
 
     return title;
 }
@@ -919,7 +925,7 @@ int gmx_genbox(int argc, char *argv[])
 #define NFILE asize(fnm)
 
     static int      nmol_ins   = 0, nmol_try = 10, seed = 1997, enum_rot;
-    static real     r_distance = 0.105, r_shell = 0;
+    static real     r_distance = 0.105, r_shell = 0, r_scale = 0.57;
     static rvec     new_box    = {0.0, 0.0, 0.0}, deltaR = {0.0, 0.0, 0.0};
     static gmx_bool bReadV     = FALSE, bCheckAllPairDist = FALSE;
     static int      max_sol    = 0;
@@ -936,6 +942,8 @@ int gmx_genbox(int argc, char *argv[])
           "Random generator seed"},
         { "-vdwd",   FALSE, etREAL, {&r_distance},
           "Default van der Waals distance"},
+        { "-vdwscale", FALSE, etREAL, {&r_scale},
+          "HIDDENScale factor to multiply Van der Waals radii from the database in share/gromacs/top/vdwradii.dat. The default value of 0.57 yields density close to 1000 g/l for proteins in water." },
         { "-shell",  FALSE, etREAL, {&r_shell},
           "Thickness of optional water layer around solute" },
         { "-maxsol", FALSE, etINT,  {&max_sol},
@@ -978,7 +986,7 @@ int gmx_genbox(int argc, char *argv[])
         /*generate a solute configuration */
         conf_prot = opt2fn("-cp", NFILE, fnm);
         title     = read_prot(conf_prot, &atoms, &x, bReadV ? &v : NULL, &r, &ePBC, box,
-                              aps, r_distance);
+                              aps, r_distance, r_scale);
         if (bReadV && !v)
         {
             fprintf(stderr, "Note: no velocities found\n");
@@ -1019,7 +1027,8 @@ int gmx_genbox(int argc, char *argv[])
     if (bInsert)
     {
         title_ins = insert_mols(opt2fn("-ci", NFILE, fnm), nmol_ins, nmol_try, seed,
-                                &atoms, &x, &r, ePBC, box, aps, r_distance, r_shell,
+                                &atoms, &x, &r, ePBC, box, aps, 
+                                r_distance, r_scale, r_shell,
                                 oenv, opt2fn_null("-ip", NFILE, fnm), deltaR, enum_rot,
                                 bCheckAllPairDist);
     }
@@ -1032,7 +1041,7 @@ int gmx_genbox(int argc, char *argv[])
     if (bSol)
     {
         add_solv(opt2fn("-cs", NFILE, fnm), &atoms, &x, v ? &v : NULL, &r, ePBC, box,
-                 aps, r_distance, &atoms_added, &residues_added, r_shell, max_sol,
+                 aps, r_distance, r_scale, &atoms_added, &residues_added, r_shell, max_sol,
                  oenv);
     }
 

diff --git a/src/gromacs/gmxlib/atomprop.c b/src/gromacs/gmxlib/atomprop.c
index 9d8aa60f85042b00ef68fa09947c6952a112d939..ed2ffbe666e6bc56565a063407535a106347499b 100644 (file)
--- a/src/gromacs/gmxlib/atomprop.c
+++ b/src/gromacs/gmxlib/atomprop.c
@@ -49,6 +49,7 @@
 #include "index.h"
 #include "strdb.h"
 #include "copyrite.h"
+#include "statutil.h"
 
 typedef struct {
     gmx_bool    bSet;
@@ -62,7 +63,7 @@ typedef struct {
 } aprop_t;
 
 typedef struct gmx_atomprop {
-    gmx_bool          bWarned;
+    gmx_bool          bWarned,bWarnVDW;
     aprop_t           prop[epropNR];
     gmx_residuetype_t restype;
 } gmx_atomprop;
@@ -284,7 +285,8 @@ gmx_atomprop_t gmx_atomprop_init(void)
 
     gmx_residuetype_init(&aps->restype);
     aps->bWarned = FALSE;
-
+    aps->bWarnVDW = FALSE;
+    
     return (gmx_atomprop_t)aps;
 }
 
@@ -329,6 +331,18 @@ void gmx_atomprop_destroy(gmx_atomprop_t aps)
     sfree(ap);
 }
 
+static void vdw_warning(FILE *fp)
+{
+    if (NULL != fp)
+    {
+        fprintf(fp,"NOTE: From version 5.0 %s uses the Van der Waals radii\n",
+                ShortProgram());
+        fprintf(fp,"from the source below. This means the results may be different\n");
+        fprintf(fp,"compared to previous GROMACS versions.\n");
+        please_cite(fp,"Bondi1964a");
+    }
+}
+
 gmx_bool gmx_atomprop_query(gmx_atomprop_t aps,
                             int eprop, const char *resnm, const char *atomnm,
                             real *value)
@@ -368,6 +382,11 @@ gmx_bool gmx_atomprop_query(gmx_atomprop_t aps,
     j = get_prop_index(&(ap->prop[eprop]), ap->restype, resname,
                        atomname, &bExact);
 
+    if (!ap->bWarnVDW)
+    {
+        vdw_warning(stdout);
+        ap->bWarnVDW = TRUE;
+    }
     if (j >= 0)
     {
         *value = ap->prop[eprop].value[j];

diff --git a/src/gromacs/gmxlib/copyrite.c b/src/gromacs/gmxlib/copyrite.c
index 1a9a61bb7cd2497971e8704f24229a2c1b164543..4915f238536998063d08d705ba720999aa06617f 100644 (file)
--- a/src/gromacs/gmxlib/copyrite.c
+++ b/src/gromacs/gmxlib/copyrite.c
@@ -485,6 +485,11 @@ void please_cite(FILE *fp, const char *key)
           "Solvation energy in protein folding and binding",
           "Nature",
           319, 1986, "199-203" },
+        { "Bondi1964a",
+          "A. Bondi",
+          "van der Waals Volumes and Radii",
+          "J. Phys. Chem.",
+          68, 1964,"441-451" },
         { "Eisenhaber95",
           "Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael Scharf",
           "The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies",