[gmx-users] Dihedral copying from itp to ff

[Raj D]

Dear Justin,
Thanks ,I am doing it to bring the ligand and protein under one molecule
type in order to apply distance restraint between atoms of ligand and amino
acids . This I am doing based on your suggestion for my earlier post
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097280.html
.
So why always pdb2gmx write topology with proper dihedral function type of
9 and how to force it to write different function type based on user entry
in ffbonded.itp file.
Regards,
Raja
On May 12, 2015 5:01 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 5/12/15 12:05 AM, Raj D wrote:
>
>> Dear User,
>> I have done MD simulation successfully with ligand.itp file produced by
>> Antechamber. Now I have to include the ff information of the ligand into
>> AMBER99SB forcefield
>> and in the process I am so for successful in creating rtp entry and bond
>> and angles parameter in ffbonded.itp file but I have struck in copying
>> dihedral parameters data from ligand.itp to ffbonded.itp files.
>>
>
> Why is any of this necessary?  You can save yourself the hassle and just
> keep the parameters in the ligand.itp file; there's no need to copy
> anything to the parent force field.
>
> -Justin
>
>  The antechamber produced dihedral type 3 ( RB ) and the grompp issue the
>> ERROR like No default Proper Dih. types for all missing new dihedral of
>> the
>> ligands ( totally 68 errors) and if I change the function type from 9 to 3
>> ( the default in the AMBER99SB ) the grompp sense the new dihedral...
>> Please help me to get out of the issue.
>> Regards,
>> Raja
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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