[gmx-users] pdb2gmx picks up the wrong .tdb files?

[Justin Lemkul]

On 1/16/20 10:07 AM, András Ferenc WACHA wrote:
>
> Dear Justin,
>
> thank you. Am I doing something wrong or is this a bug in Gromacs? Do 
> you have a suggestion how to make this work? Should I rename the 
> terminal patches or should I put everything under one basename 
> (sacrificing cleanliness and maintainability)?
>

Without spending a long time going through the code, likely what is 
happening is pdb2gmx is loading the .rtp files in alphabetical order, 
finding the first match of LYS (which occurs in your beta-amino acid 
file) and loads the matching .tdb file - this is why alpha-amino acids 
don't work; they're interpreted as beta. The cleanest solution would 
probably be to prefix your beta-amino acids to change their residue 
names, e.g. BLYS instead of LYS in both the .rtp and coordinate files.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

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