[gmx-users] Fatal error: Atom O in residue BTC 1 not found in rtp entry with 156 atoms while sorting atoms

[Justin Lemkul]

On 10/13/14 8:17 AM, Nilesh Dhumal wrote:
> Hello,
>
> I am getting a following error for pdb2gmx.
> Fatal error:
> Atom O in residue BTC 1 not found in rtp entry with 156 atoms
>               while sorting atoms
>
>
> Could anyone tell whats going wrong?
>

Atoms named O1 or O2 get translated per xlateat.dat.  Either use different 
names, change xlateat.dat, or use version 5.0 where this was fixed.

-Justin

> Nilesh
>
> Here is initial part of .pdb file
> TITLE     Title
> REMARK    THIS IS A SIMULATION BOX
> CRYST1   12.776   12.776   25.994  90.00  90.00  90.00 P 1           1
> MODEL        1
> ATOM      1  O1  BTC     1     195.790 145.610 180.060  1.00  0.00
> ATOM      2  C1  BTC     1     185.330 150.070 185.330  1.00  0.00
> ATOM      3  C2  BTC     1     178.650 161.630 178.650  1.00  0.00
> ATOM      4  C3  BTC     1     184.330 167.370 167.370  1.00  0.00
> ATOM      5  HM  BTC     1     192.150 163.580 163.580  1.00  0.00
> ATOM      6  C3  BTC     1     167.370 167.370 184.330  1.00  0.00
> ATOM      7  HM  BTC     1     163.580 163.580 192.150  1.00  0.00
> ATOM      8  O1  BTC     1     145.610 180.060 195.790  1.00  0.00
> ATOM      9  C1  BTC     1     150.070 185.330 185.330  1.00  0.00
>
>
>
> .rtp file
>   [ BTC ]
>   [ ATOMS ]
>   O1  opls_993   -0.665  1
>   C1  opls_995    0.778  3
>   C2  opls_996   -0.092  4
>   C3  opls_997   -0.014  5
>   HM  opls_998    0.109  6
>   C3  opls_997   -0.014  5
>   HM  opls_998    0.109  6
>   O1  opls_993   -0.665  1
>   C1  opls_995    0.778  3
>   C2  opls_996   -0.092  4
>   C3  opls_997   -0.014  5
>   HM  opls_998    0.109  6
>   O1  opls_993   -0.665  1
>   C1  opls_995    0.778  3
>   C2  opls_996   -0.092  4
>
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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