[gmx-users] gromacs ligand topology file for "GNP"

[Justin Lemkul]

On 9/7/17 9:23 AM, Deep kumar wrote:
> Hello,
>
> On Thu, Sep 7, 2017 at 1:11 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 9/6/17 3:46 PM, Deep kumar wrote:
>>
>>> Dear All,
>>>
>>> I have produced the "ITP" files of the ligands using ATB server.  I am
>>> mentioning the steps here, please let me know if you think anything is
>>> wrong.
>>>
>>> a) uploaded the coordinates of ligand "RND" on ATB server. I chose
>>> "heteromoelcule" molecule type.
>>>
>>> b) Entered the "net charge" by calculating like this using chimera: (added
>>> Hydrogen prior to calculating net charge and produced .mol2 file to
>>> calculate the net charge)
>>>
>>> from chimera import openModels, Molecule
>>> from AddCharge import estimateNetCharge
>>> from OpenSave import osOpen
>>> output = osOpen("charge-estimates", "w")
>>> for m in openModels.list(modelTypes=[Molecule]):
>>>           print>>output, m, m.name, estimateNetCharge(m.atoms)
>>> output.close()
>>>
>>> the "net charge" of "RND" was shown to be "2".
>>>
>>>
>> Does that make sense?  What is RND?
>
> RND is the ligand found in 4NYM.pdb file. I am trying to make a system of
> this pdb for MD.
>

I understand that; I'm trying to get you to think a little bit about the 
chemistry.  What are the titratable groups and what are their pKa 
values?  Does a +2 net charge make sense?  This would be pretty uncommon 
for any small molecule that is considered an inhibitor/ligand for a protein.

>>
>> c) submitted the entry and after completion, downloaded the file as below:
>>>   From "Molecular Dynamics(MD) files", chose "Forcefield" to be
>>> "Gromos54A7"
>>> & "Format" to be "Gromacs", and downloaded "All Atom" ITP file.
>>>
>>> I am running the MD on Gromacs version 5.1. I have prepared the protein
>>> topology using "pdb2gmx" of Gromacs using "Gromos96 54A7" force field.
>>>
>>> Please let me know if I did right or if anything else is needed to be
>>> done.
>>>
>>> Secondly, I also need .gro file of the ligand. Can you please let me know
>>> how can I get that. The tutorial am following (
>>> http://www.bevanlab.biochem.
>>> vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html) says, I
>>> have to prepare a position restraint file "posre_RND.itp" from the
>>> "RND.gro" file, so how can I get the "RND.gro" file?
>>>
>>>
>> You don't need a .gro file to generate a position restraint file; as with
>> most operations in GROMACS, you can use any coordinate file format here.
>> If you *really* want to use .gro, you can transform between formats with
>> editconf.
>>
>> And lastly, please let me know how to generate topology of "GNP" molecule
>>> with gromos53A6 FF. I tried ATB but it says error "
>>> Error recorded: Unsupported bond length encountered: 0.56nm (PA-O5'). This
>>> often indicates there is an error in the submitted structure.
>>> "
>>>
>>>
>> The error here is pretty clear.  You have a bad geometry for this molecule
>> with a bond length that is about 3 times longer than it really should be.
>> Visualizing the coordinates should make this apparent since ATB is telling
>> you exactly which bond is problematic.
>>
> Thanks, can you please let me know how can I solve this problem?

Look at the geometry - is there a problem?  Has the PDB file you're 
supplying for GNP been modified in any way?  Does it visualize 
properly?  I doubt an experimental assignment of a 0.56-nm bond would be 
made when it should be on the order of 0.16 nm or so.

-Justin

>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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