[gmx-users] Charmm to gromacs

[Abu Naser]

Thanks Justin for your response. 

I just manually inserted the input values only to that part of the script.  The atom types I am interested in, they are not available in the charmm36. Since I have only few unusual atom types, I wish to do them manually and trying to figure out how it can be converted. 







 

> Date: Fri, 8 Aug 2014 08:50:16 -0600
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Charmm to gromacs
> 
> 
> 
> On 8/8/14, 3:11 AM, Abu Naser wrote:
> > Hi All,
> >
> > I took the following from Mark's script to convert non-bonded parameters of ZN manually:
> >
> > printf("% 5s %f   0.0     A %.4g %.4g\n", $atom, $element_mass, 2*$four_epsilon * $sigma**6, $four_epsilon * $sigma**12);
> >
> >
> > I am getting:
> >
> > -0.0002245 -1.205e-08
> >
> > instead of:
> >
> > 0.194215920555  1.046
> >
> >
> > Am I missing anything?
> >
> > I would appreciate your respond.
> >
> 
> Probably something wrong with your input file.  There's no need to do these 
> conversions; we provide the latest CHARMM36 FF for Gromacs at 
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
> 
> -Justin
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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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