Jenny Hsu wrote:
Hi all:
I have a problem with grompp
I want to making "POPC+protein" file
and I search the archieve and follow the process
1.run pdb2gmx for protein only
2.add below parameters into my topology file
#include "ffG53a6.itp"
#include "lipid.itp"
#include "popc.itp"
3.adjust the [ molecules ] section to list the number and type of my
components
4.run editconf and genbox
5.run grompp and it shows
Fatal error:
Atomtype CA not found
We just had a discussion about this:
http://www.gromacs.org/pipermail/gmx-users/2008-November/038282.html
You can copy the relevant portions of lipid.itp into the appropriate sections in
ffG53a6nb.itp/ffG53a6bon.itp. Otherwise, including the files as you have will
not work.
-Justin
*Below is all information it shows*
*Can someone help me to solve this problem?*
*I am appreciate with that.*
*Thaks.*
:-) G R O M A C S (-:
Getting the Right Output Means no Artefacts in Calculating Stuff
:-) VERSION 4.0 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org <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 em.mdp Input, Opt! grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c 1UEO-nowater_water.gro Input Structure file: gro g96 pdb
tpr tpb
tpa
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
-n index.ndx Input, Opt. Index file
-p 1UEO-nowater.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o 1UEO-nowater_em.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file: edr ene
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-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.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 0 Number of allowed warnings during input
processing
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/md/share/gromacs/top/ffG53a6.itp
Opening library file /usr/local/md/share/gromacs/top/ffG53a6nb.itp
Opening library file /usr/local/md/share/gromacs/top/ffG53a6bon.itp
Opening library file /usr/local/md/share/gromacs/top/ff_dum.itp
WARNING 1 [file lipid.itp, line 14]:
Overriding atomtype LO
WARNING 2 [file lipid.itp, line 15]:
Overriding atomtype LOM
WARNING 3 [file lipid.itp, line 16]:
Overriding atomtype LNL
WARNING 4 [file lipid.itp, line 17]:
Overriding atomtype LC
WARNING 5 [file lipid.itp, line 18]:
Overriding atomtype LH1
WARNING 6 [file lipid.itp, line 19]:
Overriding atomtype LH2
WARNING 7 [file lipid.itp, line 20]:
Overriding atomtype LP
WARNING 8 [file lipid.itp, line 21]:
Overriding atomtype LOS
WARNING 9 [file lipid.itp, line 22]:
Overriding atomtype LP2
WARNING 10 [file lipid.itp, line 23]:
Overriding atomtype LP3
WARNING 11 [file lipid.itp, line 24]:
Overriding atomtype LC3
WARNING 12 [file lipid.itp, line 25]:
Overriding atomtype LC2
WARNING 13 [file lipid.itp, line 108]:
Overriding non-bonded parameters,
old: 0.00238804 3.38411e-06 new
LNL C 1 2.387718e-03 2.389594e-06
-------------------------------------------------------
Program grompp, VERSION 4.0
Source code file: toppush.c, line: 793
Fatal error:
Atomtype CA not found
--
Jenny Hsu, Biotechnology Dept.,
Ming Chuan University, Taiwan, R.O.C
------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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