[gmx-users] grompp is lying...

leafyoung81-group at yahoo.com leafyoung81-group at yahoo.com
Fri Jul 28 23:31:28 CEST 2006

You may use -pp for grompp to see what the processed top looks like. It could be true that some where, C-like directive is not correct or sections are incomplete.

Yang Ye

----- Original Message ----
From: Ken Rotondi <ksr at chemistry.umass.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Saturday, July 29, 2006 3:31:56 AM
Subject: [gmx-users] grompp is lying...

I know, enigmatic subject, but it's true.

The program is GROMACS 3.3.1 running on a Fedora linux box. I'm trying 
to do the most simple thing, charge balance a system with 1 protein and 
solvent. When I try to run grompp to generate a run input file for 
genion there is a fatal error stating that the .gro and .top files are 
not consistent and that in fact that .top file is empty. When I open 
the .top file in gedit it contains all the appropriate data for the 
protein (charges, bonds, angels, etc.) and ends with the [molecules] 
section showing two compounds, Protein_A and SOL, containing 1 and 
10703 molecule, respectively.

I moved the .pdb and .mdp file to another machine (same OS and GMX 
version) and grompp returns the same error.

I just used the first machine to generate functioning .tpr files for 
genion and md run on a huge system containing multiple chains of 
protein and RNA just a few days ago, so, I'm very confused.

Any insight would be welcome,


Commands with key output attached:

pdb2gmx -f 1WT.pdb -o WT.gro -p WT.top

There are  745 dihedrals,  698 impropers, 2071 angles
           2312 pairs,     1420 bonds and     0 virtual sites
Total mass 15456.438 a.m.u.
Total charge -4.000 e

editconf -f WT.gro -o WTbox.gro -box 7 7 7

No velocities found
     system size :  3.964  3.545  4.278 (nm)
     center      :  0.611  1.254  0.013 (nm)
     box vectors :  4.144  4.144 20.280 (nm)
     box angles  :  90.00  90.00  90.00 (degrees)
     box volume  : 348.26               (nm^3)
     shift       :  2.889  2.246  3.487 (nm)
new center      :  3.500  3.500  3.500 (nm)
new box vectors :  7.000  7.000  7.000 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 343.00               (nm^3)

genbox -cp WTbox.gro -cs spc216.gro -o WTsol.gro -p WT.top

Output configuration contains 33509 atoms in 10839 residues
Volume                 :         343 (nm^3)
Density                :     1008.26 (g/l)
Number of SOL molecules:  10703

Processing topology
Adding line for 10703 solute molecules to topology file (WT.top)

Back Off! I just backed up WT.top to ./#WT.top.1#

grompp -f lbfgsmin.mdp -c WTsol.gro -p WT.top -o ions.tpr

Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (WTsol.gro, 33509)
              does not match topology (WT.top, 0)

(Last 4 lines of the WT.top file)

[ molecules ]
; Compound        #mols
Protein_A           1
SOL             10703

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