What if you try 1000 steps at 10K with no restraints, to simplify?
Bill
On 5/13/17 11:36 PM, kungking Hanpaibool wrote:
> Dear Elvis,
>
>
>
> this is my input file. I retrained the side chain. and generated binary file.
>
> it seems to be your suggestion. but some atom move out. How can I solve this problem?
>
>
> MD heating of system over 200 ps
> &cntrl
> imin=0,
> irest=0,
> ntx=1,
> nscm=1000,
> nstlim=100, dt=0.002,
> ntpr=1, ntwx=1,
> ioutfm=1,
> iwrap=0,
> ntxo=1,
> ntwr=5000,
> ntb=1,
> cut=10.0,
> ntc=2, ntf=2,
> ntp=0,
> ntt=3,
> gamma_ln=5.0,
> ig=-1,
> ntr=1,
> restraint_wt=5.0,
> restraintmask='!:WAT&.CA,N,C,O,ZN',
> nmropt=1,
> /
> &wt
> TYPE='TEMP0', ISTEP1=0, ISTEP2=100000,
> VALUE1=10.0, VALUE2=310.0,
> /
> &wt TYPE='END' /
>
>
>
> Best Regards,
>
> kungking
>
>
> ________________________________
> From: Elvis Martis <elvis.martis.bcp.edu.in>
> Sent: Sunday, May 14, 2017 2:11 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] MCPB and Can not run MD simulation; some residue move out of protein
>
> Can you post input file? That will tell how you are heating the sytem.
>
> You can also try adding restraints to your system (protein + ligand + metal ion) during the heating to avoid the system from blowing up.
>
> use ntr = 1, and the add the residue mask.
>
> Also, if your output format is not binary (netcdf) then also add iwrap = 1.
>
> If you do not want to add iwrap flag then switch the output format to netcdf format.
>
>
>
>
> Best Regards
>
> [photo]
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
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> ________________________________
> From: kungking Hanpaibool <kunkungking.hotmail.com>
> Sent: 14 May 2017 01:35:59
> To: amber.ambermd.org
> Subject: [AMBER] MCPB and Can not run MD simulation; some residue move out of protein
>
> 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.eyJ2ZXIiOiJFeGNoYW5nZS5DYWxsYmFjay5WMSIsImFwcGN0eHNlbmRlciI6Ik93YURvd25sb2FkQDg0ZGY5ZTdmLWU5ZjYtNDBhZi1iNDM1LWFhYWFhYWFhYWFhYSIsImFwcGN0eCI6IntcIm1zZXhjaHByb3RcIjpcIm93YVwiLFwicHJpbWFyeXNpZFwiOlwiUy0xLTI4MjctMzkzMjE2LTI0Mzg4ODUzMjhcIixcInB1aWRcIjpcIjE2ODg4NTIyOTkxNDkyNjRcIixcIm9pZFwiOlwiMDAwNjAwMDAtOTE1ZS02ZmQwLTAwMDAtMDAwMDAwMDAwMDAwXCIsXCJzY29wZVwiOlwiT3dhRG93bmxvYWRcIn0iLCJpc3MiOiIwMDAwMDAwMi0wMDAwLTBmZjEtY2UwMC0wMDAwMDAwMDAwMDBAODRkZjllN2YtZTlmNi00MGFmLWI0MzUtYWFhYWFhYWFhYWFhIiwiYXVkIjoiMDAwMDAwMDItMDAwMC0wZmYxLWNlMDAtMDAwMDAwMDAwM!
> DAwL2F0dGFjaG1lbnQub3V0bG9vay5vZmZpY2UubmV0QDg0ZGY5ZTdmLWU5ZjYtNDBhZi1iNDM1LWFhYWFhYWFhYWFhYSIsImV4cCI6MTQ5NDcwNjAyMywibmJmIjoxNDk0NzA1NDIzfQ.h85lvADA6m2uBJ49yZElisjSIp1vRLp0h3Hx9rQqFUqbW5bZtz1X8rZMAet3smP47Ur4Y5A2Bxijy1VjdGCWk-G2e4FalW6A2iwSe0Jz8dvmhdgbKh2eJaU9Vgdk_znEaZanQAJFPVk26NZaHofsvcVkbHmyrKG72ncjrWqgO8tTGK05ft-wh0AeDRwokB_5NMr32Ol2H-7TN4jWzC6URF9_i0Argn8XhXcuv0GyXKpFUMOTaw7hdNvneRB7em1ul0TB5lQC1WRmn2CTLE1Foa4_-XTFwRdl_TvbaF6zloIBQlKgreNPXMeJy3HZXvLTb2eHg3VMiI6tEJcsVOl-lw&owa=outlook.live.com&isc=1]
>
> 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 Sun May 14 2017 - 00:00:03 PDT
