> On Feb 23, 2014, at 7:53 AM, Yip Yew Mun <yipy0005.gmail.com> wrote:
>
> Hi, I have done antechamber and used gaussian to get the atomic charges on the covalently bonded ligand, which is to be bonded to a cysteine residue. However, when I run leap, it could not find angle parameters such as SH-ca-ca, SH-ca-ca, CT-SH-ca. However, I’m totally unable to generate the prep file parameters containing them, as the atom names of the cysteine moiety in my antechamber files are not named like the actual cysteine residue. What can I do?
Add these parameters by hand to the frcmod file. You can look in the gaff.dat file for clues about what those parameters should be.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Feb 23 2014 - 08:00:04 PST
