[gmx-users] intermolecular distance restrains

nahren manuel meetnahren at yahoo.com
Thu Sep 2 22:29:00 CEST 2010

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.

I am able to do with -merge in the previous (ver 4.0.7 of ) pdb2gmx.


--- On Thu, 9/2/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:

From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] intermolecular distance restrains
To: "Discussion list for GROMACS users" <gmx-users at 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.


> Best,
> nahren

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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