[gmx-users] Dihedral copying from itp to ff

[Justin Lemkul]

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
>

-- 
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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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