Biswajit Gorai wrote:
Dear Bipin,
Edit your topology file as:
###########################################
; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Ion_chain_A2.itp"
*#include "oct.itp"*
If oct.itp introduces new atom types (as the original .top does, for GAFF),
placing this topology here will result in a fatal error since there is a new
[atomtypes] directive that is introduced after the protein [moleculetype]. If
oct.itp does not introduce any new atom types, its location within the system
topology is irrelevant.
; Include water topology
#include "amber99sb-ildn.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "amber99sb-ildn.ff/ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
Ion_chain_A2 1
*1-octanol 1
*
*SOL 8987*
Depending on the order of the coordinate file, it may not be possible to merge
the SOL entries in this way.
-Justin
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
