[gmx-users] gmx pdb2gmx

[Justin Lemkul]

On 9/20/18 7:21 AM, antonia vyrkou wrote:
> Hello!
>
> I want to create a topology file for a LDHA-NADH-PYRUVATE system.
> I have created the pdb file, copied the .rtp in the relevant directory and
> added a       [ bond ] and [ impropers ] section for pyruvate.
>
> When I run gmx pdb2gmx I get two warnings and a fatal error.
>
> The warnings are:
> Warning: Starting residue NAD801 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue PYR802 in chain not identified as Protein/RNA/DNA.
>
> NADH and Pyruvate are not enzymes, how should I specify them in the
> residuetypes.dat file?

These are merely advisory; they will not cause a problem as long as all 
.rtp entries are properly defined.

> The fatal error is:
> Residue 'PYR' not found in residue topology database
>
> Doesn't gmx pdb2gmx use as input the local rtp file where PYR is specified?

The .rtp file must be in the force field subdirectory that you're using.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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