[gmx-users] rtp topology file for ligand

amna khan amnakhan369 at gmail.com
Tue Feb 19 18:53:29 CET 2013 

i generated the ligand.gro by using the command

*editconf -g my_otp_ligand.pdb -o ligand.gro*
*
*
*WARNING: all CONECT records are ignored*
*Read 38 atoms*
*No velocities found*

it printed this and after this i did as mention in tutorial

it generated the bad box error  and the wc -l comand result is as follows

*and wc -l conf.gro
*
*2237 conf.gro*
*
*
*
*
*the first three lines *
*
2196
  705SER      N    1  -3.373  -1.131   1.295
  705SER     H1    2  -3.442  -1.166   1.232
  705SER     H2    3  -3.339  -1.043   1.261
  705SER     H3    4  -3.298  -1.196   1.303


and last three lines are
    0_NFP    HO   36  -0.376  -0.128   0.141
    0_NFP   C26   37  -0.328   0.137  -0.081
    0_NFP   C27   38  -0.293   0.373  -0.168
   9.21266   2.62220   3.05500


what is woring with ligand to gro converion ?

why this bad box error arose ?


regards
amna khan
*







On Tue, Feb 19, 2013 at 8:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<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/****<http://vt.edu/Pages/Personal/justin/**>
>>> gmx-tutorials/complex/index.****html<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://vt.edu/Pages/Personal/justin>
>>> <h**ttp://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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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