[gmx-users] number of coordinates in coordinate file does not match topology
Christopher Stiles
CS145331 at albany.edu
Fri Jul 20 23:30:00 CEST 2007
I get the following when running grompp:
-bash-3.00$ grompp -f mdout_test.mdp -c SWNT_6_6_144.gro -p SWNT_6_6_144.top
-o
:-) G R O M A C S (-:
God Rules Over Mankind, Animals, Cosmos and Such
:-) VERSION 3.3.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2006, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp (-:
Option Filename Type Description
------------------------------------------------------------
-f mdout_test.mdp Input, Opt! grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c SWNT_6_6_144.gro Input Generic structure: gro g96 pdb tpr tpb
tpa xml
-r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa
xml
-rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa
xml
-n index.ndx Input, Opt. Index file
-deshuf deshuf.ndx Output, Opt. Index file
-p SWNT_6_6_144.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o topol.tpr Output Generic run input: tpr tpb tpa xml
-t traj.trr Input, Opt. Full precision trajectory: trr trj
-e ener.edr Input, Opt. Generic energy: edr ene
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first after this time.
-np int 1 Generate statusfile for # nodes
-[no]shuffle bool no Shuffle molecules over nodes
-[no]sort bool no Sort molecules according to X coordinate
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-load string Releative load capacity of each node on a
parallel machine. Be sure to use quotes around
the string, which should contain a number for
each node
-maxwarn int 10 Number of warnings after which input processing
stops
-[no]check14 bool no Remove 1-4 interactions without Van der Waals
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...
calling cpp...
processing topology...
processing coordinates...
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448
Fatal error:
number of coordinates in coordinate file (SWNT_6_6_144.gro, 144)
does not match topology (SWNT_6_6_144.top, 0)
-------------------------------------------------------
"You're Insignificant" (Tricky)
These of the commands I use to get to that point:
x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp
***Note: for some reason it does not generate SWNT_6_6_144.rtp
editconf -f SWNT_6_6_144.gro -o SWNT_6_6_144.gro -d 0.5
genbox -cp SWNT_6_6_144.gro -cs -o SWNT_6_6_144_b4em.gro -p
SWNT_6_6_144.top -maxsol 300
grompp -f mdout_test.mdp -c SWNT_6_6_144.gro -p SWNT_6_6_144.top -o
Also I notice that after running grompp it over writes the top file with:
# 1 "ffG43b1.n2t"
# 1 "<built-in>"
# 1 "<command line>"
# 1 "ffG43b1.n2t"
C C 1 C ; CNT Carbon with one bond
C C 2 C C ; CNT double bonded Carbon
O O 1 C ; CARBONYL OXYGEN (C=O)
O OM 1 C ; CARBOXYL OXYGEN (CO-)
O OA 2 C H ; HYDROXYL OXYGEN (OH)
O OW 2 H H ; WATER OXYGEN
N N 3 H C C ; PEPTIDE NITROGEN (N OR NH)
N NT 3 H H C ; TERMINAL NITROGEN (NH2)
N NL 4 C H H H ; TERMINAL NITROGEN (NH3)
N NR5 2 C C ; AROMATIC N (5-RING,2 BONDS)
N NR5* 3 C C H ; AROMATIC N (5-RING,3 BONDS)
N NP 3 C C FE ; PORPHYRIN NITROGEN
C C 3 C O * ; BARE CARBON (PEPTIDE,C=O,C-N)
; Note that order is importante here because of wildcards.
C C3 4 H H H * ; ALIPHATIC CH3 GROUP
C C2 4 H H C * ; ALIPHATIC CH2 GROUP
C C1 4 H C * * ; ALIPHATIC CH GROUP
C CB 3 C C C ; BARE CARBON (5-,6-RING)
H H 1 N ; HYDROGEN BONDED TO NITROGEN
H HO 1 O ; HYDROXYL HYDROGEN
H HW 1 OW ; WATER HYDROGEN
H HS 1 S ; HYDROGEN BONDED TO SULFUR
Any help or advice is greatly appreciated!
~Christopher Stiles
College of Nanoscale Science and Engineering (CNSE)
State University of New York, Albany, New York 12203, USA
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