hi
the error message is here:
WARNING: There is a bond of 6.744147 angstroms between:
------- .R<CYX 137>.A<CB 5> and .R<CYX 198>.A<O 10>
This is a known bug in pdb4amber in AT17 that incorrectly write the CONECT
record.
You can either
1. delete the wrong CONECT record in the output pdb and explicitly create
the bond between S-S
e.g: http://ambermd.org/tutorials/advanced/tutorial18/section1.htm
2. correct the CONECT field.
PS: Other might have better experience about tleap.
Hai
On Sun, Nov 12, 2017 at 6:14 PM, jacky zhao <jackyzhao010.gmail.com> wrote:
>
> Hi
> Â We have used AT17 to generate the parm7 and crd files. The error
> message
> indicated that the CYX may not be recognized properly. I have attached
> the
> error message and pdb file below.
> However, the same pdb file can generate parm7 and crd files by using
> AT16.
> Anyone can give some suggestions?
> Thank you for taking your time.
> ååµå¾ç 1 Â
> --
> Lei Zhao, Ph.D.
> International Joint Cancer Institute of the Second Military Medical
> University
> National Engineering Research Center for Antibody Medicine
> New Library Building 11th floor,800 Xiang Yin Road
> Shanghai 200433
> P.R.China
>
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Received on Sun Nov 12 2017 - 17:00:02 PST
