[gmx-users] Re: pdb2gmx error

[Shima Arasteh]

Dear Justin,
Again, I appreciate you. I learn much from you, feeling happy :)

Thanks a lot.

 
Sincerely,
Shima


----- Original Message -----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Wednesday, June 27, 2012 10:10 PM
Subject: Re: [gmx-users] Re: pdb2gmx error



On 6/27/12 1:35 PM, Shima Arasteh wrote:
> I know it's much better to use a non-deprecated ff.  But what could I do? I have to regenerate the results of simulation done by gmx.ff . Aren't there any solution to pass this step?

I have no idea how to make gmx.ff work.  I "solved" the issue by commenting out the line and seeing that no error resulted.  This, of course, isn't an actual solution, just a debugging method.  The force field defines its impropers in an odd way, and as such I don't know that there is a workaround.

> 
> I PROMISE YOU AND ME TO REPEAT THE SIMULATION WHIT A MODERN FF AS SOON AS POSSIBLE :)
> 

The sooner, the better.  This is an ancient force field, and vastly better parameter sets exist.

-Justin

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

Justin A. Lemkul, Ph.D.
Research Scientist
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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