[gmx-users] rtp topology file for ligand

[amna khan]

yes i am following this tutorial too

this is my topology file for the ligand i made by atb

*http://compbio.biosci.uq.edu.au/atb/download.py?molid=7045

*
*from here i got the .itp file and optimzed ligand.pdb file but what about
the .gro file and .top file
*
*i ran that command to make the .gro and .top file of ligand ....
*
*this is as follows
*

pdb2gmx -f my_ligand_opt.pdb -o my_ligand.gro -i my_ligand_posre.itp -p
my_ligand.top.

this generated the fetal error

Fatal error:
Residue 'LIG' not found in residue topology database

SO WHAT SHOULD I DO ABOUT THIS PROBLEM


On Tue, Feb 19, 2013 at 5:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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