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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