[gmx-users] rtp topology file for ligand

[Justin Lemkul]

On 2/19/13 10:53 AM, amna khan wrote:
> 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
>

Follow the tutorial more closely.  pdb2gmx will not deal with your ligand, so 
remove its coordinates from the protein-ligand complex and only run the protein 
through pdb2gmx.  You do not need pdb2gmx to make a topology for the ligand - 
you already have the topology in .itp format from ATB.  If you need the ligand 
coordinates in .gro format, simply transform from .pdb to .gro using edticonf. 
The job of pdb2gmx is to produce a topology, an output coordinate file is a side 
effect.

You do not need a separate .top file for the ligand.  A .top file is a system 
topology, encompassing all elements of the system and thus there can only be 
one.  Other molecules (like your ligand) are #included in the system .top file 
using .itp format.

-Justin

>
> 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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-- 
========================================

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

========================================