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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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