[gmx-users] Seeking solution for the error "Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms while sorting atoms".

[Justin Lemkul]

On 9/6/13 8:52 AM, Santhosh Kumar Nagarajan wrote:
> Hi guys,
>
> My problem is in the first step itself.
>
>
> "Fatal error:
> Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms
> while sorting atoms."
>
> I understand that the problem is with the .rtp database. But. My doubt
> is how to create a new rtp entry for that missing residue.
>

I doubt you need to.  The presence of OXT indicates a C-terminal residue - is 
Trp323 in fact the C-terminus or is the structure malformed?  What are you 
choosing for your C-terminus type when running pdb2gmx?  A full command would be 
useful here, as would telling us which force field you are trying to use.

-Justin

> The following is the portion of my pdb containing the error(OXT).
>
> ATOM    591  N   TRP D 323      10.307  18.558 238.142  1.00 99.84           N
> ATOM    592  CA  TRP D 323       9.202  18.123 237.287  1.00101.69           C
> ATOM    593  C   TRP D 323       9.168  16.586 237.258  1.00102.94           C
> ATOM    594  O   TRP D 323       9.051  16.019 236.150  1.00102.73           O
> ATOM    595  OXT TRP D 323       9.259  15.996 238.358  1.00 -1.00           O1-
> ATOM    596  CB  TRP D 323       9.296  18.792 235.895  1.00 -1.00           C
> ATOM    597  CG  TRP D 323       9.208  20.290 235.866  1.00 -1.00           C
> ATOM    598  CD1 TRP D 323       8.072  21.009 235.721  1.00 -1.00           C
> ATOM    599  CD2 TRP D 323      10.289  21.267 235.969  1.00 -1.00           C
> ATOM    600  NE1 TRP D 323       8.370  22.356 235.739  1.00 -1.00           N
> ATOM    601  CE3 TRP D 323      11.693  21.183 236.123  1.00 -1.00           C
> ATOM    602  CE2 TRP D 323       9.724  22.577 235.890  1.00 -1.00           C
> ATOM    603  CZ3 TRP D 323      12.492  22.342 236.195  1.00 -1.00           C
> ATOM    604  CZ2 TRP D 323      10.510  23.741 235.965  1.00 -1.00           C
> ATOM    605  CH2 TRP D 323      11.903  23.619 236.118  1.00 -1.00           C
> ATOM    606  H   TRP D 323      11.186  18.079 238.010  1.00  0.00           H
> ATOM    607  HA  TRP D 323       8.251  18.419 237.732  1.00 -1.00           H
> ATOM    608  HB2 TRP D 323      10.221  18.496 235.398  1.00 -1.00           H
> ATOM    609  HB3 TRP D 323       8.488  18.416 235.267  1.00 -1.00           H
> ATOM    610  HD1 TRP D 323       7.087  20.577 235.614  1.00 -1.00           H
> ATOM    611  HE1 TRP D 323       7.661  23.070 235.652  1.00 -1.00           H
> ATOM    612  HE3 TRP D 323      12.160  20.211 236.188  1.00 -1.00           H
> ATOM    613  HZ3 TRP D 323      13.562  22.249 236.313  1.00 -1.00           H
> ATOM    614  HZ2 TRP D 323      10.050  24.715 235.903  1.00 -1.00           H
> ATOM    615  HH2 TRP D 323      12.521  24.503 236.177  1.00 -1.00           H
>
> Help me to solve this
>
> Thanks in advance
>
> Regards,
> Santhosh
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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