ram bio wrote:
Dear Gromacs Users,
I have generated the topology and parameters files for my ligand
through swiss param site. Now i am trying to run a simulation of
protein ligand complex in POPC bilayer using OPLS force field in
Gromacs, but when I am using the grompp command in gromacs for tpr
generation I am getting an error as follows:
I've not used SwissParam, but it advertises itself as a means to generate CHARMM
parameters, not OPLS. So it sounds like you're mixing force fields, which is
not appropriate.
Atomtype C5A not found
Please let me know your suggestions, to correct this error, I have
included ligand.itp in the topology file of the protein.
The ligand.itp file probably utilizes atomtypes that are not present in OPLS-AA.
This should be your first hint that you're doing something you shouldn't.
-Justin
Thanks,
ram
grompp -f mdions.mdp -c combi.gro -p topol.top -o combi.tpr
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14#
checking input for internal consistency...
NOTE 1 [file mdions.mdp, line unknown]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.
processing topology...
Opening library file
/usr/local/gromacs-4.0.7-single/share/gromacs/top/ffoplsaa.itp
Opening library file
/usr/local/gromacs-4.0.7-single/share/gromacs/top/ffoplsaanb.itp
Opening library file
/usr/local/gromacs-4.0.7-single/share/gromacs/top/ffoplsaabon.itp
Generated 348195 of the 348195 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 348005 of the 348195 1-4 parameter combinations
Opening library file /usr/local/gromacs-4.0.7-single/share/gromacs/top/tip3p.itp
Opening library file /usr/local/gromacs-4.0.7-single/share/gromacs/top/ions.itp
-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 947
Fatal error:
Atomtype C5A not found
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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