James Starlight wrote:
Thanks, Justin
I'll test your program soon.
Today also I have some problems with generation of the posre for lipids
I have lipid bilayer in pdb. Then I selected one lipid molecule and move
it to separate pdb and convert it to gro via editconf.
Than I've used genres and generate posre file for 1 lipid. Than I
include tis posre to topology of my bilayer
using gropt I obtain eror that I'm using wrong posre topology
Also I've tried to include posre.itp to my lipid.itp ( this file contain
link to posre on default) This run didnt produce any errors but as the
result posres have not been worked ( I obtained perturbed bilayer after
minimization)
How I can generate work posre for my bilayer to prevent perturbation
after equilibration or minimization ?
Since posre.itp is the default name given to the protein position restraint file
by pdb2gmx, the first step is to use a different name. Then, you have to add
the new #include statement in the correct location in the topology. Presuming
you do that, the lipids should be restrained in whatever manner you've specified.
-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
