[AMBER] The force constants of bond and angle items are zero when the MCPB program reads the internal force constant matrix

From: JiYuan Liu <liujiyuan.nwsuaf.edu.cn>
Date: Mon, 13 May 2013 15:43:43 +0800

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   Hello,
   I encountered a problem about deal with dual-core manganese metalloprotein
   complex by MCPB program in Ambertools11,some force constants of bond and
   angle items in *_md.frcmod are zero when the MCPB program reads the internal
   force constant matrix(Z-matrix method),but the *_sem.frcmod was derived from
   Seminario Method is ok.I also checked the file 1AMP_OH_md.frcmod generated
   in the tutorial example 1AMP,It was found that three force constants of
   angle item was zero.so I uploaded my results(the md.frcmod and sem.frcmod)
   and the tutorial example(1AMP_OH_md.frcmod and 1AMP_OH_sem.frcmod) in the
   attachment.
   What kind of help me.
   1. Whether these situations is normal?
   2. Which force constants parameters are more suitable for Molecular
   Dynamics,*_md.frcmod or *_sem.frcmod?
   Thank you very much.
   Best Regards
   JiYuan
   --
   Jiyuan Liu
   Key Laboratory of Plant Protection Resources and Pest Management,National
   Ministry of Education
   Northwest A&F University
   Yangling, Shaanxi
   China 712100
   Phone: 86-29-87092190

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Received on Mon May 13 2013 - 01:00:02 PDT
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