On 10/14/13 2:44 AM, Sathya wrote:
Hi,
I'm doing the KALP-15 IN DPPC through the Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
After generating the new position restrain file, I start to energy
minimization to get the correct area per lipid. As below:
Scale the lipid positions by a factor of 4:
perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
LOOP :
Energy minimization with restrained protein
grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
-maxwarn 1.
after using the above command I got error like this
Fatal error:
[ file strong_posre.itp, line 143 ]:Atom index (139) in position_restraints
out of bounds (1-138).
This probably means that you have inserted topology section
"position_restraints" in a part belonging to a different molecule than you
intended to. In that case move the "position_restraints" section to the
right molecule.
Please help me how to solve this
You created the restraint file wrong. Please follow the tutorial exactly.
-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
==================================================
--
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
