Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private tutor. I am CC'ing the list and ask that further comments and
questions be posted there.
On 2/26/13 8:40 AM, Group Gro wrote:
Dear Prof. Justin,
Thanks a lot about your recommendation. We couldn't solve the mentioned problem
so we send the pdb file which we have used.
Note that the residue numbering starts with 38, and since pdb2gmx's internal
numbering starts from 1, you have to account for that when interpreting the
output it gives you in the error. Thus, if you consider residue 87, you will
find several missing atoms (which is also true of residue 88):
ATOM 385 N GLU A 87 23.475 -6.728 -18.885 1.00 0.00 N
ATOM 386 CA GLU A 87 24.447 -5.778 -19.407 1.00 0.00 C
ATOM 387 C GLU A 87 24.781 -6.087 -20.882 1.00 0.00 C
ATOM 388 O GLU A 87 24.937 -5.173 -21.682 1.00 0.00 O
ATOM 389 CB GLU A 87 25.739 -5.810 -18.551 1.00 0.00 C
ATOM 390 CG GLU A 87 26.807 -4.816 -19.030 1.00 0.00 C
ATOM 391 N GLU A 88 24.914 -7.371 -21.218 1.00 0.00 N
ATOM 392 CA GLU A 88 25.294 -7.785 -22.573 1.00 0.00 C
ATOM 393 C GLU A 88 24.208 -7.557 -23.624 1.00 0.00 C
ATOM 394 O GLU A 88 24.492 -7.121 -24.756 1.00 0.00 O
ATOM 395 CB GLU A 88 25.710 -9.249 -22.567 1.00 0.00 C
ATOM 396 CG GLU A 88 26.979 -9.513 -21.726 1.00 0.00 C
Note that both of the glutamates are missing their carboxylate side chain atoms.
You should carefully inspect the remainder of the file for any other missing
atoms.
We apologize for asking another question that we have faced. When we want to
make a itp file and gro file for ligand or drug, we use The /PRODRG/ Server
<http://www.google.com/url?sa=t&rct=j&q=prodrg&source=web&cd=1&cad=rja&sqi=2&ved=0CC8QFjAA&url=http%3A%2F%2Fdavapc1.bioch.dundee.ac.uk%2Fprodrg%2F&ei=zLksUe920cuzBoLPgOgD&usg=AFQjCNHYWpbCiIJn8ZJm20-DQmDEFGDBHg&bvm=bv.42965579,d.Yms>but
it seemes that the reated files aren't correct. For examplein a ligand, some of
Hydrogen atomes(CH2) are regarded united! Is there any other way to make itp and
gro files for ligand or drug?
As PRODRG advertises, it produces topologies intended for use with the GROMOS96
family of force fields, which are united-atom force fields. PRODRG produces
unreliable topologies, making ATB a better choice for GROMOS96 parameters
(though one should carefully validate any topology produced by any of these
automated methods, though ATB is significantly better than PRODRG). Parameters
for ligands can be created for any force field, either via online servers or
contributed programs on the Gromacs website. Please consult the list archive;
these topics are discussed routinely.
-Justin
Thanks alot.
ali kazemi
department of biochemistry
islamic azad university shahrekord branch
--------------------------------------------------------------------------------
*From:* Justin Lemkul <jalem...@vt.edu>
*To:* Group Gro <group...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org>
*Sent:* Monday, February 25, 2013 5:02 PM
*Subject:* Re: [gmx-users] request
On 2/25/13 6:09 AM, Group Gro wrote:
>
>
>
> Dear Gromacs Users.
>
>
> I apologize for asking a question that has come up several times by numerous
users in the previous e-mails, but I have read the answers and suggestions to
those posts and I am not still able to solve the problem based on them. It is
completely possible that I am just not seeing the obvious, so I apologize, but I
would welcome any advice. I want to work on "Human Glutathione Peroxidase" and
downloaded its pdb file, but when I try pdb2gmx, I face Fatal Error:
>
> Program pdb2gmx, VERSION 4.5.5
> Source code file:
> /build/buildd/gromacs-4.5.5/src/kernel/pgutil.c, line: 91
> Fatal error:
> Atom CD is used in an interaction of
> type atom in the topology
> database, but an atom of that name was
> not found in residue
> number 50.
>
>
> I tried different force fields, for example OPLS-AA/L all-atom force field,
different versions of AMBERs, but I
> always get the same problem! When I tried GROMOS's versions, the problem goes
on CZ atom instead of CD. Here is a chunk of my pdb file (I have also attached
the full pdb file to this e-mail):
>
> SHEET 6 A 1 PHE A 183 PRO A190 0
> SHEET 7 A 1 GLY A 192 HIS A200 0
> MODEL
> ATOM 1 N GLY A 38 -4.242 -9.833 -26.316 1.00 0.00 N
> ATOM 2 CA GLY A 38 -3.416 -10.949 -25.765 1.00 0.00 C
> ATOM 3 C GLY A 38 -1.953 -10.570 -25.632 1.00 0.00 C
> ATOM 4 O GLY A 38 -1.069
> -11.266 -26.159 1.00 0.00 O
> ATOM 5 N THR A 39 -1.673 -9.461 -24.940 1.00 0.00 N
> ATOM 6 CA THR A 39 -0.286 -9.039 -24.705 1.00 0.00 C
> ATOM 7 C THR A 39 -0.073 -8.722 -23.214 1.00 0.00 C
> ATOM 8 O THR A 39 -1.035 -8.559 -22.442 1.00
> 0.00 O
> ATOM 9 CB THR A 39 0.124 -7.784 -25.533 1.00 0.00 C
> ATOM 10 OG1 THR A 39 -0.415 -6.602 -24.926 1.00 0.00 O
> ATOM 11 CG2 THR A 39 -0.309 -7.882 -27.037 1.00 0.00 C
> …..
> ATOM 91 OD1 ASP A 49 10.106 1.841 -5.471 1.00 0.00 O
> ATOM 92 OD2 ASP A 49 12.010 2.918 -5.273 1.00 0.00 O
> ATOM 93 N GLY A 50 8.192 0.495 -3.643 1.00 0.00 N
> ATOM 94 CA GLY A 50 6.805 0.919 -3.449 1.00 0.00 C
> ATOM 95 C GLY A 50 6.525 2.278 -4.054 1.00 0.00 C
> ATOM
> 96 O GLY A 50 5.449 2.818 -3.864 1.00 0.00 O
> ATOM 97 N GLU A 51 7.471 2.832 -4.802 1.00 0.00 N
> ATOM 98 CA GLU A 51 7.351 4.238 -5.211 1.00 0.00 C
> ATOM 99 C GLU A 51 6.737 4.438 -6.592 1.00 0.00 C
> ATOM 100 O GLU A
> 51 6.291 5.522 -6.897 1.00 0.00 O
> ATOM 101 CB GLU A 51 8.713 4.941 -5.174 1.00 0.00 C
> ATOM 102 CG GLU A 51 9.283 5.140 -3.759 1.00 0.00 C
> ATOM 103 CD GLU A 51 8.612 6.301 -3.006 1.00 0.00 C
> ATOM 104 N GLU A 52 6.729
> 3.418 -7.432 1.00 0.00 N
> ….
> ATOM 3035 OH TYR A 228 -9.320
> -43.377 -52.577 1.00 0.00 O
> TER 3036 TYR A 228
> ENDMDL
> HETATM 3037 CL CL 11000 -16.070
> -39.525 -6.168 1.00 0.00 CL
> HETATM 3038 NA NA 11001 -1.679
> -34.065 -0.491 1.00 0.00 NA
> CONECT 996 1519
> CONECT 1021 1519
> CONECT 1519 996 1021
> END
>
> I know that the residue number printed
> by pdb2gmx is actually starting from zero, so the problem is actually in GLU.
> In both rtp file and pdb I have CD atom. Some suggestions wanted to
> change the order of C and O in pdb file, but it didn't work. What should I
do?
Your statements are inconsistent. You say above that changing the force field
triggers a problem with a different atom (CZ instead of CD), which doesn't make
much sense. The amino acids have standard atom nomenclature, so changing the
force field should not change the error. Beyond that, the real reason is that
you're missing an atom somewhere and the PDB header should have clearing
"MISSING" lines that tell you exactly what that is. If you need further help
diagnosing, providing the actual PDB code would be helpful.
-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
========================================
--
========================================
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
