Now I have deleted HXT lines in the PDB files and performed the simulation.
Any one have some suggestions?
Thanks a lot.
Jacky
2017-09-13 18:28 GMT+08:00 jacky zhao <jackyzhao010.gmail.com>:
> Hi everyone
> When I was using tleap to generate parm7 crd files for simulation, these
> were some errors. I have attached below:
>
> Thank you for taking your time
>
>
> Loading PDB file: ./wt_for_simulation.pdb
> Created a new atom named: HXT within residue: .R<CALA 115>
> Added missing heavy atom: .R<CALA 115>.A<OXT 11>
> Created a new atom named: HXT within residue: .R<CGLU 229>
> Added missing heavy atom: .R<CGLU 229>.A<OXT 16>
> total atoms in file: 3610
> Leap added 2 missing atoms according to residue templates:
> 2 Heavy
> The file contained 2 atoms not in residue templates
> Since added/missing = extra, there is a high probability
> of atoms with 'incorrect' names; you may want to
> use addPdbAtomMap to map these names, or change in file
>
>
> --
> 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
>
--
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 13 2017 - 05:30:04 PDT
