[gmx-users] Charmm to gromacs

[Justin Lemkul]

On 8/8/14, 9:18 PM, Abu Naser wrote:
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> 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

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>> 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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>   		 	   		
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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

==================================================