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

[András Ferenc WACHA]

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.

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
>
-- 
András Ferenc Wacha, PhD
research fellow, CREDO instrument responsible

Biological Nanochemistry Research Group (310)

Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences (RCNS)
Magyar tudósok körútja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.hu
CREDO SAXS instrument: http://credo.ttk.hu


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