[gmx-users] 4-letter residues

[Justin Lemkul]

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

==================================================