[gmx-users] intermolecular distance restrains

[Justin A. Lemkul]

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 /<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.
> 
>     -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
> 
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> 

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

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

========================================