[gmx-users] Re: pdb2gmx error
shima_arasteh2001 at yahoo.com
Wed Jun 27 19:48:58 CEST 2012
Again, I appreciate you. I learn much from you, feeling happy :)
Thanks a lot.
----- Original Message -----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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