[gmx-users] problem in simulation of DMPC lipid bilayer

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 25 12:10:03 CET 2009

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.


> 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


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