[gmx-users] Query- Ligand parametrization

[Justin Lemkul]

On 3/28/15 7:05 AM, Priya Das wrote:
> I am sorry to bother again and again.  I am new to it and still learning
> the basics.
> My molecule is a decahydroquinoline. The paramchem generated .str file is
> HERE
> <https://cgenff.paramchem.org/initguess/filedownload.php?file=20150328/Pose1.str>
> .

That file is not accessible.  I'm not sure why there are high penalties in that 
molecule; it is very straightforward.

> I am following CGennFF tutorial and your instructions as HERE
> <http://mackerell.umaryland.edu/~kenno/cgenff/program.html>. As penalties
> are there i need to use QM, but i am not able to run CHARMM simulations as
> CHARMM is not freely available. So tried to use this Toolkit
> <http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/>, but still in vain.
>

Because neither CHARMM nor fftk do what you need to do.  You need QM software 
that is capable of doing geometry optimizations, angle and dihedral scans, and 
vibrational analysis.  We use Gaussian.  If you don't have access to that kind 
of software, you're not going to be able to generate the target data you need, 
simply put.

On the MM side, assuming you can generate the QM target data for refinement, any 
package will work - CHARMM, GROMACS, etc.  You don't explicitly need CHARMM. 
You need something that can do energy minimization and single-point energy 
evaluations.

-Justin

-- 
==================================================

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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