Hi Kungking,
Please check the frcmod file generated by MCPB.py to see whether there are some wired parameters in it. If there are some, there are two potential reasons to cause this: (1) the structure dissociates after the QM optimization or (2) you rearranged atom sequence of the QM optimization (makes it different from the small model fingerprint file). You can fix the problem based on its real situation.
Kind regards,
Pengfei
> On May 13, 2017, at 3:05 PM, kungking Hanpaibool <kunkungking.hotmail.com> wrote:
>
> Dear Amber staff,
>
>
> I try to use MCPB.py to generate the metalloprotein and already got the prmtop and pdb. But When I try to run md simulation.
>
> in Heating step, it showed
>
> (try to print out every 1 step and the result showed like below)
>
>
>
> NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = NaN PRESS = 0.0
> Etot = NaN EKtot = NaN EPtot = **************
> BOND = ************** ANGLE = 688184.4339 DIHED = 15445.5362
> 1-4 NB = 318454.5089 1-4 EEL = -716.7853 VDWAALS = **************
> EELEC = -243053.9862 EHBOND = 0.0000 RESTRAINT = **************
> EAMBER (non-restraint) = **************
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ===============================================================================
>
> So I display it by VMD and found that there are some atom move out of the protein, showed like this picture
>
> [https://attachment.outlook.office.net/owa/kunkungking.hotmail.com/service.svc/s/GetFileAttachment?id=AQMkADAwATYwMAItOTE1ZS02ZmQwLTAwAi0wMAoARgAAA6u6yYYJAQlBgtvIolBNU8cHAKFNzIUONHZKns1xYxbhGnIAAAIBDwAAAKFNzIUONHZKns1xYxbhGnIAAADel10nAAAAARIAEAAv5E6bgLwXQoTPR7Gz38Q0&X-OWA-CANARY=xlr_HFtR4kmbbjYmckg1BxAWXF46mtQYzT5s52TX3VL5Uikw1AEF-Ygu0zVbY-GYEC-V5n4a00E.&token=eyJ0eXAiOiJKV1QiLCJhbGciOiJSUzI1NiIsIng1dCI6ImVuaDlCSnJWUFU1aWpWMXFqWmpWLWZMMmJjbyJ9.eyJ2ZXIiOiJFeGNoYW5nZS5DYWxsYmFjay5WMSIsImFwcGN0eHNlbmRlciI6Ik93YURvd25sb2FkQDg0ZGY5ZTdmLWU5ZjYtNDBhZi1iNDM1LWFhYWFhYWFhYWFhYSIsImFwcGN0eCI6IntcIm1zZXhjaHByb3RcIjpcIm93YVwiLFwicHJpbWFyeXNpZFwiOlwiUy0xLTI4MjctMzkzMjE2LTI0Mzg4ODUzMjhcIixcInB1aWRcIjpcIjE2ODg4NTIyOTkxNDkyNjRcIixcIm9pZFwiOlwiMDAwNjAwMDAtOTE1ZS02ZmQwLTAwMDAtMDAwMDAwMDAwMDAwXCIsXCJzY29wZVwiOlwiT3dhRG93bmxvYWRcIn0iLCJpc3MiOiIwMDAwMDAwMi0wMDAwLTBmZjEtY2UwMC0wMDAwMDAwMDAwMDBAODRkZjllN2YtZTlmNi00MGFmLWI0MzUtYWFhYWFhYWFhYWFhIiwiYXVkIjoiMDAwMDAwMDItMDAwMC0wZmYxLWNlMDAtMDAwMDAwMDAwMDAwL2F0dGFjaG1lbnQub3V0bG9vay5vZ
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>
> the display showed OH of Threonine move out of the protein.
> for the pdb file which was generated by prmtop. it's quite correct.
> I don't know , Which step were I wrong. Could you suggest me for solve this problem?
>
> Best Regards,
> Kungking
>
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Received on Thu May 18 2017 - 10:00:02 PDT
