On 6/20/12 11:25 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
yes I have already seen this site, but want I meant is that I have no idea
which values I should set. Is there something like a standard for dummy
protein for membrane?
No. You have to decide what these dummy atoms are and how they might (or might
not) interact with the system and what parameters (if any) they have. If
they're completely non-interacting then there's not really any reason to have them.
-Justin
Eva
On 6/20/12 10:17 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I try to use GROMACS for my protein where I added a layer of dummy atoms
simulating the membrane around it.
But now when I want to call "pdb2gmx" I always get the error:
Fatal error:
Residue 'DUM' not found in residue topology database
I understand the error, that there is no entry for the dummy residue in
the .tpr file. But is there a possibility to add it there. Because the
file don't look like that I can just write "DUM" in it.
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
-Justin
my pdb file looks like this:
ATOM 2597 CB LEU A 313 12.816 -29.877 -23.547 1.00 55.31
C
ATOM 2598 CG LEU A 313 14.261 -29.695 -23.059 1.00 54.06
C
ATOM 2599 CD1 LEU A 313 15.169 -30.640 -23.866 1.00 53.26
C
ATOM 2600 CD2 LEU A 313 14.757 -28.257 -23.179 1.00 54.46
C
TER
HETATM 3076 DUM DUM A 314 -4.000 -49.000 6.000 1.00 1.70
HETATM 3077 DUM DUM A 314 -4.000 -49.000 7.000 1.00 1.70
HETATM 3078 DUM DUM A 314 -4.000 -48.000 6.000 1.00 1.70
HETATM 3079 DUM DUM A 314 -4.000 -48.000 7.000 1.00 1.70
.
.
.
.
HETATM 36213 O HOH A 527 25.281 -35.299 13.147 1.00 37.03
O
HETATM 36214 O HOH A 528 46.452 -27.955 -20.733 1.00 19.63
O
HETATM 36215 O HOH A 530 32.439 -23.614 -26.720 1.00 27.12
O
TER
Best regards,
Eva
--
========================================
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
========================================
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--
========================================
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
========================================
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