[gmx-users] Re: pdb2gmx error

[Justin A. Lemkul]

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

-- 
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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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