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

[Deep kumar]

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.


>
>
> 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?


>
> -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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>