[gmx-users] rtp topology file for ligand

[Justin Lemkul]

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

-- 
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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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