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
--
========================================
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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