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.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
pY2UubmV0QDg0ZGY5ZTdmLWU5ZjYtNDBhZi1iNDM1LWFhYWFhYWFhYWFhYSIsImV4cCI6MTQ5NDcwNjAyMywibmJmIjoxNDk0NzA1NDIzfQ.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 - 00:00:02 PDT
