I think I should change the atom type N5,N6 to NB(last mail I am wrong).But there is still error:
Error occured on rank 1.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
CalcError: /usr/local/amber12/bin/sander failed with prmtop com.top!
Error occured on rank 7.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 7
bad atom type: NB
CalcError: /usr/local/amber12/bin/sander failed with prmtop com.top!
Error occured on rank 3.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
bad atom type: NB
bad atom type: NB
bad atom type: NB
bad atom type: NB
Did I think it too simple？I really need your help.
------------------ 原始邮件 ------------------
发件人: "wenjuanli93";<wenjuanli93.gmail.com>;
发送时间: 2015年4月12日(星期天) 下午2:09
收件人: "AMBER Mailing List"<amber.ambermd.org>; "amber"<amber.ambermd.org>;
主题: [AMBER] 回复：Re: Bad atom Type in MMPBSA.py
Dear Kenneth, Thanks for your reply.I am trying other ways because I dont have permission to do that. After the md production done,I modify the .top file (change the N5,N6 back to ND1 atom) and use this file to run ante-MMPBSA.py.I dont know if it's right to do that. wjli
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Received on Sun Apr 12 2015 - 00:30:02 PDT
