On 7/30/14, 2:59 AM, RINU KHATTRI wrote:
check your topology file weather any coordinate is missing in your topology
basically in angles region check your ffnonbonded.itp you have been pasted
the line from lipid.itp or not
This issue is not related to coordinates or parameters from any lipid force
field.
-Justin
On Wed, Jul 30, 2014 at 12:15 AM, John Doe <helstr...@hotmail.com> wrote:
Hi,
I'm attempting to simulate "polyethylene" using OPLS (I'm using Gromacs
5.0.1-dev). I'm using the files from:
https://www.mail-archive.com/gmx-users@gromacs.org/msg19683.html
I have moved the OPLS force field directory to my working directory and
placed "ffoplsaa.rtp" and "ffoplsaa.hdb" in the OPLS directory. I use
pdb2gmx (selecting the option for OPLS in my folder) to produce the gro and
top files
"""
gmx pdb2gmx -f polyethylene.pdb -o PE_processed.gro
"""
This works fine. I think enlarge the simulation box:
"""
gmx editconf -f PE_processed.gro -o PE_bigBox.gro -bt cubic -c -d 2.0
"""
Again, works fine. I then move on to energy minimize using the mdp file
from:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/minim.mdp
However, when I run grompp:
gmx grompp -f minim.mdp -c PE_bigBox.gro -p topol.top -o PE_minim.tpr
I get the following error:
"""
ERROR 1 [file topol.top, line 162]:
No default Proper Dih. types
ERROR 2 [file topol.top, line 163]:
No default Proper Dih. types
ERROR 3 [file topol.top, line 164]:
No default Proper Dih. types
ERROR 4 [file topol.top, line 165]:
No default Proper Dih. types
ERROR 5 [file topol.top, line 166]:
No default Proper Dih. types
"""
I'm not quite sure why I'm getting this error because the dihedral are
defined in OPLS. Take for instance ERROR 1. This
error correlates to the dihedral "HC-CT-CT-CT", however, in the OPLS
bonded parameters file, the dihedral is written out as "CT-CT-CT-HC", so
I'm not sure why grompp is not processing this. Does this dihedral
need to be reversed? Then ERROR 2 corresponds to "CT-CT-CT-CT" which is
defined in the bonded parameters (file "ffbonded.itp"). So I'm not really
sure what's going on.
Thanks for the help.
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--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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