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

[Justin Lemkul]

On 1/17/20 4:25 AM, András Ferenc WACHA wrote:
> Dear Justin,
>
> there are no name clashes in the .rtp files by design, I never re-use
> already existing residue names. Beta3-homo-lysine is B3K,
> beta2-homo-lysine is B2K, and disubstituted amino-acids also have their
> naming scheme.

Sorry, no idea. This should work out of the box, because it's the normal 
behavior in force fields that have e.g. aminoacids.rtp, dna.rtp, etc. 
with matching .tdb files. Without access to the force field to dig into 
it, there's not much I can suggest other than putting everything into 
merged.rtp, merged.*.tdb, etc.

-Justin

> Andras
>
> On 1/16/20 11:34 PM, Justin Lemkul wrote:
>>
>> 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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