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Isn't Mark's script outdated for this purpose?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
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