On 2/19/13 4:23 AM, amna khan wrote:
hi all,
i generated the .itp file for my ligand using ATB,
and i have generated the protein topology file by using the forcefield 13
my question is i need to generate the *ligand .top and .gro files*
and when i use the command
*pdb2gmx -f lig.pdb -o igand.gro -i lig.itp -p iig.top
*
*the error arises that
Fatal error:
Residue 'LIG' not found in residue topology database
*
what should i do ?
how to create the rtp file for my ligand ... i have read the tutorail but i
am not getting it what steps* exactly should i do please please help me and
guide me in making the .rtp file for my ligand
*
Chapter 5 of the manual describes .rtp format, but you don't need it. You
already have a ligand topology from ATB, so why ask pdb2gmx to do it over again?
Remove the ligand from the coordinate file and deal with it separately. I
don't know which tutorial you're referring to, but you should at least try to
follow the protocol I describe here:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
-Justin
--
========================================
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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