lammps lammps wrote:
Hi everyone,
The structural formula of PEO is CH3-- O- CH2 - CH2 - (O - -CH2 - CH2 )n
- O - -CH2 - CH2 - O - CH3
I have obtain all the OPLS-AA FF for PEO from a paper such as
atomtypes, bondtypes, angletypes, and dihedraltypes. Then I have a .PDB
of PEO. I need a residuce to create .top and .gro.
The questions are
1. What is the suitable residuce datebase of PEO I must create
myselt for the command pdb2gmx conversing PDB to .top and .gro?
Read the manual for the appropriate format. In addition, this link might
provide some general guidance:
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html
2. If there is a suitable residuce, what file should I change except
the ffoplsaa.rtp?
Perhaps the .hdb, if you are missing any hydrogen atoms.
-Justin
Any suggestion is appreciated. Thanks in advance.
--
wende
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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