Hi,
Thanks for your reply.
I solved the problem after I've modified the residue name.
It was CYM（deprotonated-S），and the tleap results indicated that no type for any atom of CYM.
It is LIG now, and I get the parameters of this ligand.
the pdb file as follow,
HETATM 1 N LIG A 2 12.843 9.931 -7.615 0.90 28.58 N1+
HETATM 2 CA LIG A 2 12.969 8.842 -8.653 0.90 29.40 C
HETATM 3 C LIG A 2 12.810 9.459 -10.055 0.90 28.84 C
HETATM 4 O LIG A 2 11.768 8.921 -11.006 0.90 26.35 O
HETATM 5 CB LIG A 2 11.912 7.750 -8.388 0.90 36.02 C
HETATM 6 SG LIG A 2 10.239 8.444 -8.401 0.90 39.13 S1-
HETATM 7 OXT LIG A 2 13.707 10.597 -10.485 0.90 26.17 O1-
HETATM 8 H1 LIG A 2 12.975 9.492 -6.604 1.00 0.00 H
HETATM 9 H2 LIG A 2 11.839 10.400 -7.684 1.00 0.00 H
HETATM 10 H3 LIG A 2 14.007 8.376 -8.581 1.00 0.00 H
HETATM 11 H4 LIG A 2 12.105 7.290 -7.363 1.00 0.00 H
HETATM 12 H5 LIG A 2 11.997 6.938 -9.184 1.00 0.00 H
HETATM 13 H6 LIG A 2 13.622 10.703 -7.789 1.00 0.00 H
TER 14
END
Best,
Yuan
> -----原始邮件-----
> 发件人: "David A Case" <david.case.rutgers.edu>
> 发送时间: 2018-08-16 00:48:56 (星期四)
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 抄送:
> 主题: Re: [AMBER] HOW to type a free CYS molecule
>
> On Wed, Aug 15, 2018, MinYuan wrote:
> >
> > I tried to use antechamber and parmchk2 to type this CYS, HS-CH2-CH(HN3+)-COO-.
> > But failed.
>
> Just saying "failed" doesn't provide information that would allow anyone
> to help. Can you exactly what you did, and what the result was?
>
> ....dac
>
>
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Received on Wed Aug 15 2018 - 19:30:02 PDT
