[gmx-users] OPLS-AA with TIP4P water, error during energy minimization

[Sunita Patel]

Dear gmx_users,

I am trying to simulate a protein with explicit TIP4P water by using
OPLS-AA all atom force field. I am doing it in gromacs version 3.2.1. The
crystal structure of the protein has crystallized water.

pdb2gmx -f *.pdb -p *.top -o *.gro -ss -water TIP4P

while doing pdb2gmx I got following warning message
===========================  pdb2gmx =============================================
There are 2391 dihedrals,  199 impropers, 1626 angles
          2347 pairs,      906 bonds and     0 dummies
Total mass 6517.563 a.m.u.
Total charge 6.000 e
Writing topology
Processing chain 2 (60 atoms, 60 residues)
Opening library file /usr/local/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 60 donors and 60 acceptors
There are 11 hydrogen bonds
Checking for duplicate atoms....
Now there are 60 residues with 240 atoms
Making bonds...
Warning: Short Bond (1-4 = 0 nm)
Warning: Short Bond (5-8 = 0 nm)
Warning: Short Bond (9-12 = 0 nm)
Warning: Short Bond (13-16 = 0 nm)
Warning: Short Bond (17-20 = 0 nm)
Warning: Short Bond (21-24 = 0 nm)
Warning: Short Bond (25-28 = 0 nm)
Warning: Short Bond (29-32 = 0 nm)
Warning: Short Bond (33-36 = 0 nm)
Warning: Short Bond (37-40 = 0 nm)
Warning: Short Bond (41-44 = 0 nm)
Warning: Short Bond (45-48 = 0 nm)
Warning: Short Bond (49-52 = 0 nm)
Warning: Short Bond (53-56 = 0 nm)
Warning: Short Bond (57-60 = 0 nm)
Warning: Short Bond (61-64 = 0 nm)
Warning: Short Bond (65-68 = 0 nm)
Warning: Short Bond (69-72 = 0 nm)
Warning: Short Bond (73-76 = 0 nm)
Warning: Short Bond (77-80 = 0 nm)
Warning: Short Bond (81-84 = 0 nm)
Warning: Short Bond (85-88 = 0 nm)
Warning: Short Bond (89-92 = 0 nm)
Warning: Short Bond (93-96 = 0 nm)
Warning: Short Bond (97-100 = 0 nm)
Warning: Short Bond (101-104 = 0 nm)
Warning: Short Bond (105-108 = 0 nm)
Warning: Short Bond (109-112 = 0 nm)
Warning: Short Bond (113-116 = 0 nm)
Warning: Short Bond (117-120 = 0 nm)
Warning: Short Bond (121-124 = 0 nm)
Warning: Short Bond (125-128 = 0 nm)
Warning: Short Bond (129-132 = 0 nm)
Warning: Short Bond (133-136 = 0 nm)
Warning: Short Bond (137-140 = 0 nm)
Warning: Short Bond (141-144 = 0 nm)
Warning: Short Bond (145-148 = 0 nm)
Warning: Short Bond (149-152 = 0 nm)
Warning: Short Bond (153-156 = 0 nm)
Warning: Short Bond (157-160 = 0 nm)
Warning: Short Bond (161-164 = 0 nm)
Warning: Short Bond (165-168 = 0 nm)
Warning: Short Bond (169-172 = 0 nm)
Warning: Short Bond (173-176 = 0 nm)
Warning: Short Bond (177-180 = 0 nm)
Warning: Short Bond (181-184 = 0 nm)
Warning: Short Bond (185-188 = 0 nm)
Warning: Short Bond (189-192 = 0 nm)
Warning: Short Bond (193-196 = 0 nm)
Warning: Short Bond (197-200 = 0 nm)
Warning: Short Bond (201-204 = 0 nm)
Warning: Short Bond (205-208 = 0 nm)
Warning: Short Bond (209-212 = 0 nm)
Warning: Short Bond (213-216 = 0 nm)
Warning: Short Bond (217-220 = 0 nm)
Warning: Short Bond (221-224 = 0 nm)
Warning: Short Bond (225-228 = 0 nm)
Warning: Short Bond (229-232 = 0 nm)
Warning: Short Bond (233-236 = 0 nm)
Warning: Short Bond (237-240 = 0 nm)
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Number of bonds was 180, now 180
Generating angles, dihedrals and pairs...
There are    0 dihedrals,    0 impropers,  180 angles
             0 pairs,      180 bonds and     0 dummies
Total mass 1080.924 a.m.u.
Total charge 0.000 e
Including chain 1 in system: 892 atoms 58 residues
Including chain 2 in system: 240 atoms 60 residues
Now there are 1132 atoms and 118 residues
Total mass in system 7598.487 a.m.u.
Total charge in system 6.000 e

Writing coordinate file...
==============================================================================

Even with this warning message I proceed with editconf and genbox. There
is no warning during this steps. But while performing grompp for energy
minimization I got following fetal error


===========================   grompp ====================================
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 243951 of the 243951 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 243951 of the 243951 1-4 parameter combinations
Excluding 3 bonded neighbours for Protein 1
Excluding 2 bonded neighbours for SOL 60
Excluding 2 bonded neighbours for SOL 7088
WARNING 1 [file "4pti.top", line 8422]:
  System has non-zero total charge: 6.000000e+00

processing coordinates...
Fatal error: number of coordinates in coordinate file (solvation.gro,
29724)
             does not match topology (4pti.top, 29484)

====================================================================

So what could be the reason for this error.
Thank for any suggestion.

regards,
Sunita
-------------------------------------------------------------------------------
Sunita Patel
Biophysical Lab.,
Dept. of Chemistry,
Indian Institute of Technology(IIT) Bombay,
Powai, Mumbai, Maharashtra,
INDIA-400076.

Tel: (91)-22-25764176.
Email:sunita at chem.iitb.ac.in
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