On 8/30/12 9:23 PM, Katrina Lexa wrote:
Hello Gromacs Users:
I apologize for asking a question that has come up several times in the
forum, but I have read the answers to those posts and I am not still
unable to fix the error based on the suggestions in the previous emails.
It is completely possible that I am just not seeing the obvious, so I
apologize,
but I would welcome any advice. I just have a methylated glycine that I
would like to use (SAR) within a
peptide with the AMBER force field, but when I try to build the cyclic
compound it writes out:
Opening force field file ./amber99sb_lipid.ff/atomtypes.atp
Atomtype 1
Reading residue database... (amber99sb_lipid)
Opening force field file ./amber99sb_lipid.ff/aminoacids.rtp
Residue 100
Sorting it all out...
Opening force field file ./amber99sb_lipid.ff/aminoacids.hdb
Back Off! I just backed up topol.top to ./#topol.top.59#
Processing chain 1 'A' (85 atoms, 11 residues)
Identified residue ALA1 as a starting terminus.
Identified residue ALA11 as a ending terminus.
9 out of 9 lines of specbond.dat converted successfully
Opening force field file ./amber99sb_lipid.ff/aminoacids.arn
Checking for duplicate atoms....
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.5
Source code file: pgutil.c, line: 91
Fatal error:
Atom CB is used in an interaction of type atom in the topology
database, but an atom of that name was not found in residue
number 7.
However, my residue 7 should not have a CB atom, I'm not seeing it in my
pdb file or the .rtp file (impropers section or otherwise). Perhaps that
residue is being skipped, but all of my atoms are "ATOM" rather than
HETATM, and I don't have any tabs messing up the fields.
this is the SAR (residue 7) section in my .rtp file
[ SAR ]
[ atoms ]
N N -0.22670 1
CN CT -0.22340 2
HN1 H 0.10210 3
HN2 H 0.10210 4
HN3 H 0.10210 5
CA CT -0.02520 6
HA2 H1 0.06980 7
HA3 H1 0.06980 8
C C 0.59730 9
O O -0.56790 10
[ bonds ]
N CN
N CA
CA C
CA HA2
CA HA3
CN HN1
CN HN2
CN HN3
C O
-C N
[ impropers ]
-C CA N H
CA +N C O
and here is a chunk of my pdb file
MODEL 1
ATOM 1 N ALA A 1 -5.608 1.167 2.062 1.00 0.00
N1+
ATOM 2 CA ALA A 1 -4.930 0.579 3.183 1.00 0.00
C
ATOM 3 CB ALA A 1 -5.857 0.458 4.396 1.00 0.00
C
ATOM 4 C ALA A 1 -3.814 1.597 3.525 1.00 0.00
C
ATOM 5 O ALA A 1 -4.063 2.822 3.391 1.00 0.00
O
ATOM 6 N MLE A 2 -2.575 1.132 3.819 1.00 0.00
N
ATOM 7 CN MLE A 2 -2.315 -0.257 4.265 1.00 0.00
C
ATOM 8 CA MLE A 2 -1.398 2.052 3.941 1.00 0.00
C
ATOM 9 CB MLE A 2 -1.091 2.218 5.462 1.00 0.00
C
ATOM 10 CG MLE A 2 -2.145 2.883 6.382 1.00 0.00
C
ATOM 11 CD1 MLE A 2 -1.689 2.877 7.897 1.00 0.00
C
ATOM 12 CD2 MLE A 2 -2.626 4.302 5.946 1.00 0.00
C
....
ATOM 45 N ABA A 6 4.961 4.195 -6.289 1.00 0.00 N
ATOM 46 CA ABA A 6 5.219 4.813 -7.615 1.00 0.00 C
ATOM 47 CB ABA A 6 6.627 4.541 -8.037 1.00 0.00 C
ATOM 48 CG ABA A 6 7.673 5.523 -7.418 1.00 0.00 C
ATOM 49 C ABA A 6 4.374 4.037 -8.636 1.00 0.00 C
ATOM 50 O ABA A 6 4.360 2.841 -8.453 1.00 0.00 O
ATOM 51 N SAR A 7 3.818 4.705 -9.676 1.00 0.00 N
ATOM 52 CN SAR A 7 4.087 6.071 -9.873 1.00 0.00 C
ATOM 53 CA SAR A 7 2.929 3.969 -10.548 1.00 0.00 C
ATOM 54 C SAR A 7 1.449 4.131 -10.258 1.00 0.00 C
ATOM 55 O SAR A 7 0.975 5.236 -10.559 1.00 0.00 O
ATOM 56 N MLE A 8 0.814 3.165 -9.517 1.00 0.00 N
ATOM 57 CN MLE A 8 1.365 1.822 -9.318 1.00 0.00 C
ATOM 58 CA MLE A 8 -0.491 3.432 -8.917 1.00 0.00 C
ATOM 59 CB MLE A 8 -1.599 2.488 -9.538 1.00 0.00 C
ATOM 60 CG MLE A 8 -2.739 3.173 -10.337 1.00 0.00 C
ATOM 61 CD1 MLE A 8 -3.758 3.767 -9.396 1.00 0.00 C
ATOM 62 CD2 MLE A 8 -2.404 4.282 -11.348 1.00 0.00 C
ATOM 63 C MLE A 8 -0.439 3.310 -7.362 1.00 0.00 C
ATOM 64 O MLE A 8 0.107 2.398 -6.778 1.00 0.00 O
...
Thank you for your advice,
If I recall correctly, the residue number printed by pdb2gmx is actually the
residue index (starting from zero), so the problematic residue is MLE, which
does have CB.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
