On 6/20/12 12:13 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
With the *nb.itp file you ment the "ffnonbonded.itp" file, right?
Yes. Thomas was referring to the old nomenclature of force field files.
But there is one thing:
Of course you are right, I can modify the .top file and add my Dummy atom
there. But because I got this error I mentioned, the pdb2gmx didn't
produce a .gro file.
pdb2gmx is not generally suited for dealing with complex systems, though in some
cases it does work. It is for this reason that one does not typically provide,
for instance, a protein in water with ions and some ligand to pdb2gmx. You
create the protein topology with pdb2gmx, and then add in whatever else is
necessary (solvent, ions, other molecules) and simply #include their parameters
using .itp files.
-Justin
Bests, Eva
'pdb2gmx' is mainly a tool to get the topology for (bigger) molecules
from a *.pdb file. 'pdbgmx' is expecting an entry in the *.rtp file for
the dummy atoms. You could add one in that file... (see further below)
But if the dummys only interact via nonbonded interactions it would be
more convient to write the topology by hand.
In the *.top file, you would need after the protein a new entry with
[ moleculetype ]
and
[ atoms ]
But you should also have this nonbonded interaction in the *nb.itp and
file of your force field and the atom definition in the *.atp file.
If there are also bonded parameters the new *.rtp entry would be better.
For this look at the definition of an aminoacid, or a single molecule
and write something similar for your dummy atoms.
Essential you would need the atoms definitions and charges, and then an
entry for which atoms is bonded to which.
But you should also have these interactions (nonbonded and bonded) in
the *nb.itp and *bon.itp files of your force field and the atom
definition in the *.atp file.
The basic informations for both ways are in chapter 5 of the manual.
Hope this gives some hints.
Greetings
Thomas Schlesier
Am 20.06.2012 16:18, schrieb gmx-users-requ...@gromacs.org:
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.
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
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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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