[gmx-users] intermolecular distance restrains
Justin A. Lemkul
jalemkul at vt.edu
Thu Sep 2 23:48:59 CEST 2010
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?
> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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