[gmx-users] 4-letter residues

[João Henriques]

Absolutely spot on Justin! I just discovered it by myself 30 seconds ago.

Thanks!
João

On Thu, Jul 13, 2017 at 4:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/13/17 10:16 AM, João Henriques wrote:
>
>> Dear all,
>>
>> I have a protein with a phosphorylated threonine and the corresponding
>> residue name in my FF of interest is THP1. 4-letter residues and PDB files
>> are a recipe for disaster, but somehow pdb2gmx detects the residue's name
>> and number perfectly. What happens next is somewhat odd (at least to me).
>> It now ends in a fatal error regarding OXT atoms. This should not occur
>> and, in fact, the problem disappears as soon as I use the same exact PDB
>> but with a regular non-phosphorylated threonine residue instead. The OXT
>> atoms are still there. Anyone has any idea of what's going on? Should I
>> edit the FF to use a three letter name instead of THP1?
>>
>>
> You probably forgot to add THP1 as a Protein residue in residuetypes.dat,
> so pdb2gmx is inserting an incorrect chain termination before it.
>
> -Justin
>
>
> I'm using gmx 5.1.4.
>>
>> This is the THP1 residue in my PDB:
>>
>> ATOM   1171  N   THP1A 160      14.798   3.634  55.810  1.00 28.16
>>    N
>> ATOM   1172  CA  THP1A 160      13.457   3.397  56.297  1.00 32.05
>>    C
>> ATOM   1173  CB  THP1A 160      13.440   2.416  57.453  1.00 31.31
>>    C
>> ATOM   1174  CG2 THP1A 160      12.002   2.135  57.857  1.00 28.13
>>    C
>> ATOM   1175  OG1 THP1A 160      14.038   1.189  57.027  1.00 35.99
>>    O
>> ATOM   1176  P   THP1A 160      15.501   0.748  57.510  1.00 37.49
>>    P
>> ATOM   1177  O1P THP1A 160      15.810  -0.350  56.582  1.00 38.61
>>    O
>> ATOM   1178  O2P THP1A 160      16.325   1.972  57.300  1.00 35.09
>>    O
>> ATOM   1179  OT  THP1A 160      15.173   0.306  58.890  1.00 40.70
>>    O
>> ATOM   1180  C   THP1A 160      12.747   4.659  56.712  1.00 39.18
>>    C
>> ATOM   1181  O   THP1A 160      13.202   5.412  57.567  1.00 38.80
>>    O
>>
>> This is the error:
>>
>> Fatal error:
>> Atom OXT in residue LEU 298 was not found in rtp entry LEU with 19 atoms
>> while sorting atoms.
>>
>> Thank you in advance,
>> Best regards,
>> João
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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