[email protected] wrote:
Hi Justin,
I did not mention that I am indeed trying run Gromacs implementing the
MARTINI force field. I realize this is not as automatic as selecting
other force fields in Gromacs using pdb2gmx. This issue has been
previously discussed in:
http://www.mail-archive.com/[email protected]/msg14945.html
Did you follow the actual tutorial on the MARTINI site? You should not ever
have to invoke pdb2gmx. Topology generation is conducted using MARTINI-specific
scripts. In the future, it will save a lot of time (both yours and ours) if you
provide complete, legitimate information. After all, you do not want to use
Gromos96, but your first post clearly stated that you were trying to use this
force field. If you want free help, make it easy for us to do so.
-Justin
-Lili
On 25 March 2010 18:13, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
[email protected] <mailto:[email protected]> wrote:
Dear GMX users,
I have a quick question regarding which Gromacs force field in
pdb2gmx is best suited for creating a topology (itp) file for
the enzyme, lactate oxidase. So far the force fields in Gromacs
4.0.4 are:
0: GROMOS96 43a1 force field
1: GROMOS96 43a2 force field (improved alkane dihedrals)
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
6: [DEPRECATED] Gromacs force field (see manual)
7: [DEPRECATED] Gromacs force field with hydrogens for NMR
8: Encad all-atom force field, using scaled-down vacuum charges
9: Encad all-atom force field, using full solvent charges
I selected the "G53a6 GROMOS96 53a6 Forcefield" for creating my
itp file, however, when I try to run grompp to generate the .tpr
file, I get the error:
-------------------------------------------------------
Program grompp_d, VERSION 4.0.4
Source code file: toppush.c, line: 947
Fatal error:
Atomtype Qd not found
-------------------------------------------------------
I've looked into other discussions on this
(http://www.mail-archive.com/[email protected]/msg15722.html),
and concluded that the atomtype Qd must not be present in the
G53a6 force field. My system is simply the protein lactate
oxidase. Does anyone have suggestions on which force field(s)
is best suited for this molecule?
Since the atom type "Qd" is not present in the 53a6 parameter set,
this error has nothing to do with the appropriateness of your force
field choice. Somewhere, you've incorporated a nonsensical atom
type. The only time I have ever seen "Qd" is in the MARTINI coarse
grain force fields. Be sure you're using the topologies you think
you are; if you really are using an unaltered pdb2gmx-generated
topology for 53a6, there is no way that this atom type would be
found therein.
-Justin
Thanks in advance,
Lili
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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 [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
