[gmx-users] Charmm to gromacs

[Abu Naser]

Thank you Justin. This is very useful for me. I have a question regarding 

>(and by -1 since CHARMM specifies these values as negative, but Gromacs uses a different >convention)







 I have been wondering what is the Gromacs' convention. Is it just the +ve value after conversion? 


> Date: Sat, 9 Aug 2014 03:39:07 -0600
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Charmm to gromacs
> 
> 
> 
> On 8/8/14, 9:18 PM, Abu Naser wrote:
> >
> >
> >
> > 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.
> >
> 
> It appears that the script uses the C6/C12 approach instead of specifying sigma 
> and epsilon.  That is not how we converted the CHARMM36 files.  The conversion 
> factors are a simple matter of units.  Epsilon is in kcal/mol and needs to be in 
> kJ/mol, so multiply by 4.184 (and by -1 since CHARMM specifies these values as 
> negative, but Gromacs uses a different convention).  For sigma, CHARMM specifies 
> Rmin/2 directly, but can be converted by multiplying by 2 (to get Rmin), then 
> multiplying by 2^(-1/6) (to get sigma), then multiplying by 0.1 (to convert A->nm).
> 
> -Justin
> 
> >
> >
> >
> >
> >
> >
> >
> >
> >> 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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> >   		 	   		
> >
> 
> -- 
> ==================================================
> 
> 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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