nahren manuel wrote:
Dear Gromacs Users,
The problem actually is mine is a hexamer, ARBSCT (chains). I want RST
to be merged into a single molecular topology. I am either able to merge
RS or ST or RT but not the trimer as such.
How is the .pdb set up? Does it have both chain ID's and TER delimiters? What
was your pdb2gmx command line?
-Justin
I am able to do with -merge in the previous (ver 4.0.7 of ) pdb2gmx.
Best,
nahren
--- On *Thu, 9/2/10, Justin A. Lemkul /<jalem...@vt.edu>/* wrote:
From: Justin A. Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] intermolecular distance restrains
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Date: Thursday, September 2, 2010, 8:09 PM
nahren manuel wrote:
> Dear Gromacs Users,
>
> I am presently using gromacs4.5 beta(since I want implicit
solvent). I
No need to use a beta version, the official 4.5 has been released.
> wish to apply intermolecular distance restraints.
> To my surprise there is no merge option in pdb2gmx (although
pdb2gnx -h, says it has). So is there a new alternative to create
intermolecular distance restrains.
>
Use pdb2gmx -chainsep.
-Justin
> Best,
> nahren
>
>
-- ========================================
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
</mc/compose?to=gmx-us...@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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
</mc/compose?to=gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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/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/mailing_lists/users.php
