[gmx-users] The problem of converting CGenff parameters to those of Gromacs

[David van der Spoel]

On 2012-10-15 16:53, Peter C. Lai wrote:
> Isn't Mark's script outdated for this purpose?

I just uploaded a new script that seems to work:

http://www.gromacs.org/@api/deki/files/185/=charmm2gromacs-pvm.py

Please check the comment on 
http://www.gromacs.org/Downloads/User_contributions/Other_software

>
> charmm forcefields specify epsilon and sigmas so you only need to convert
> them:
>
> gromacs(sigma) = (charmm(Rmin/2)/10) * (2/(2^(1/6)))
> gromacs(epsilon) = charmm(eps) * 4.184
>
> For 1-4 pair interactions,
> gromacs(sigma1,4 i,j) = (charmm(Rmin/2_1,4_i) + charmm(Rmin/2_1,4_j))/(2^1/6)
>
> gromacs(eps1,4 i,j) = sqrt(charmm(eps_1,4_i) * charmm(eps_1,4_j)) * 4.184
>
> On 2012-10-15 07:27:51AM -0700, spin wrote:
>> Hello, everyone.
>>
>> I used the Mark's script's to convert the CGenff (version 2b7 ) parameter
>> file to Gromacs .itp files. In the ffcharmmnb.itp, the script gave the c6
>> and c12, while the charmm's ffnonbond.itp showed  epsilon and sigma.I do not
>> understand the relation between the  c6/c12 and epsilon and sigma, and I
>> have a poor Perl skill. Can someone give me a solution?  In addition, the
>> script makes all atoms' charge zero in the file, which is not the case in
>> the ffnonbond.itp. Why is it?
>>
>> Thank you!
>>
>> Qing Liu
>>
>>
>>
>> --
>> View this message in context: http://gromacs.5086.n6.nabble.com/The-problem-of-converting-CGenff-parameters-to-those-of-Gromacs-tp5002042.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se