Mark Abraham wrote:
nitu sharma wrote:
Dear all,
I am using DMPC lipid bilayer from teleman sir
website to insert my protein in this lipid bilayer .I have done this
by using command genbox. After that when I have run the command -
pdb2gmx -f tap-in-dmpc.pdb -o tap-in-dmpc.gro -p tap-in-dmpc.top -i
tap-in-dmpc-itp -ff oplsaa
Error like this-
There are 0 hydrogen bonds
Warning: 'DMP' not found in residue topology database, trying to use
'DMSO'
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.3
Source code file: pdb2gmx.c, line: 429
Fatal error:
Atom C1 in residue DMSO 1 not found in rtp entry with 10 atoms
while sorting atoms
-------------------------------------------------------
so please tell me how can I add DMP in residue topology database if
anyone has knowledge about this. And please if also u know about any
site of lipid bilayer from where i can download lipid bilayer then let
me know.
You may find some helpful information
http://wiki.gromacs.org/index.php/Membrane_Simulations and
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
In addition to the above, which provide excellent background reference, consult
the list archives for more stepwise instructions. What you will need to do is
run pdb2gmx on *only* your protein, then modify the resulting topology to
include parameters for dmpc. Again, the archive documents how to do this, it
just takes some patience and persistence to find the right information.
-Justin
Mark
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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