On 10/24/13 1:03 AM, JuYeon wrote:
dear gromacs users
im using gromacs to make CS2 MD programs i made pdb file (by converting mol
file to pdb file) and rtp file for CS2this is what i made
<pdb file>
COMPND UNNAMEDAUTHOR GENERATED BY OPEN BABEL 2.3.2HETATM 1 C LIG
1 19.882 -4.263 -0.027 1.00 0.00 C HETATM 2 S LIG
1 21.256 -5.103 -0.054 1.00 0.00 S HETATM 3 S LIG
1 18.508 -3.424 0.000 1.00 0.00 S CONECT 1 2 3
CONECT 2 1
CONECT 3 1
MASTER 0 0 0 0 0 0 0 0
3 0 3 0END
-------------------------------------------------------------------------------------
<rtp file>
[ LIG ] [ atoms ]C opls_77 0 0S1 opls_202 0 0S2 opls_202
0 0
[ bonds ]C S1C S2
i attached rtp file to /usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp andi
added it to residuetypes.dat (which is in /usr/share/gromacs/top)then i wrote
command pdb2gmx to make gro file but it failed
Fatal error:Atom type opls_77 (residue LIG) not found in atomtype databaseFor
more information and tips for troubleshooting, please check the GROMACSwebsite
at http://www.gromacs.org/Documentation/Errors
before i made rtp file, i checked atomtypes atp file which is in oplsaa.ff it
says olps_77 is carbon(isobutene) and opls_202 is sulfides i dont know why
gromacs cant find atom type opls_77
opls_77 does not exist. opls_077 does. The bigger problem is that you should
probably not be mixing OPLS-UA parameters (opls_077) with OPLS-AA (opls_202). I
suspect a better model can be built from self-consistent parameters.
also, to make rtp file how to give charge and charge group to each atoms?
Refer to the 2001 OPLS-AA paper for the details of the required QM calculations.
The charge group is simple; the whole molecule (since it is only 3 atoms) can
be one group.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
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
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