<html><head><style type="text/css"><!-- DIV {margin:0px} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">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.<br><br>Regards,<br>Yang Ye<br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">----- Original Message ----<br>From: Ken Rotondi <ksr@chemistry.umass.edu><br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Sent: Saturday, July 29, 2006 3:31:56 AM<br>Subject: [gmx-users] grompp is lying...<br><br><div>I know, enigmatic subject, but it's true.<br><br>The program is GROMACS 3.3.1 running on a Fedora linux box. I'm trying <br>to do the most simple thing, charge balance a system with 1 protein and <br>solvent. When I
try to run grompp to generate a run input file for <br>genion there is a fatal error stating that the .gro and .top files are <br>not consistent and that in fact that .top file is empty. When I open <br>the .top file in gedit it contains all the appropriate data for the <br>protein (charges, bonds, angels, etc.) and ends with the [molecules] <br>section showing two compounds, Protein_A and SOL, containing 1 and <br>10703 molecule, respectively.<br><br>I moved the .pdb and .mdp file to another machine (same OS and GMX <br>version) and grompp returns the same error.<br><br>I just used the first machine to generate functioning .tpr files for <br>genion and md run on a huge system containing multiple chains of <br>protein and RNA just a few days ago, so, I'm very confused.<br><br>Any insight would be welcome,<br><br>Ken<br><br>Commands with key output attached:<br><br><br><br>pdb2gmx -f 1WT.pdb -o WT.gro -p WT.top<br><br>There are 745 dihedrals, 698
impropers, 2071 angles<br> 2312 pairs, 1420 bonds and 0 virtual sites<br>Total mass 15456.438 a.m.u.<br>Total charge -4.000 e<br><br><br>editconf -f WT.gro -o WTbox.gro -box 7 7 7<br><br>No velocities found<br> system size : 3.964 3.545 4.278 (nm)<br> center : 0.611 1.254 0.013 (nm)<br> box vectors : 4.144 4.144 20.280 (nm)<br> box angles : 90.00 90.00 90.00 (degrees)<br> box volume : 348.26 (nm^3)<br> shift
: 2.889 2.246 3.487 (nm)<br>new center : 3.500 3.500 3.500 (nm)<br>new box vectors : 7.000 7.000 7.000 (nm)<br>new box angles : 90.00 90.00 90.00 (degrees)<br>new box volume : 343.00 (nm^3)<br><br><br>genbox -cp WTbox.gro -cs spc216.gro -o WTsol.gro -p WT.top<br><br>Output configuration contains 33509 atoms in 10839 residues<br>Volume : 343 (nm^3)<br>Density : 1008.26 (g/l)<br>Number of SOL molecules: 10703<br><br>Processing
topology<br>Adding line for 10703 solute molecules to topology file (WT.top)<br><br>Back Off! I just backed up WT.top to ./#WT.top.1#<br><br><br>grompp -f lbfgsmin.mdp -c WTsol.gro -p WT.top -o ions.tpr<br><br>-------------------------------------------------------<br>Program grompp, VERSION 3.3.1<br>Source code file: grompp.c, line: 448<br><br>Fatal error:<br>number of coordinates in coordinate file (WTsol.gro, 33509)<br> does not match topology (WT.top, 0)<br>-------------------------------------------------------<br><br>(Last 4 lines of the WT.top file)<br><br>[ molecules ]<br>; Compound #mols<br>Protein_A 1<br>SOL 10703<br><br>_______________________________________________<br>gmx-users mailing
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