[gmx-users] generate .top file

[Justin A. Lemkul]

Mark Abraham wrote:
> On 25/12/2010 2:32 PM, shikha agarwal wrote:
>> hello
>> Merry Christmas.....
>>
>> this is my topol_pope.top file
>> ; Include chain topologies
>> #include "forcefield.itp"
>> #include "pope.itp"
>>
>> ; Include water topology
>> #include "spc.itp"
>>
>> ; Include ion topologies
>> #include "ions.itp"
>>
>> ; System specifications
>> [ system ]
>> 340-Lipid POPE Bilayer
>>
>> [ molecules ]
>> ; molecule name nr.
>> POPE 340
>> SOL 6729
>>
>>
>> but it should contain protein molecule .what should be topology file 
>> ,, how to generate that for system.gro according to tutorial. my 
>> protein has  344 molecules .
>>  I tried to use g_x2top but it is not available for gromos53a6.
> 
> You need an .itp file for your protein, and to #include it, and to 
> adjust the [molecules] field suitably.
> 

Or use the approach described in the membrane protein tutorial, wherein pdb2gmx 
is used to produce the protein .top, which is then modified to #include the 
relevant chain topologies.  It appears that the OP is claiming to use the 
tutorial but is not actually following its instructions.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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