Dear List,
I am trying to simulate a protein on a hydroxyapatite surface (141 x 146 x
27.8 A). I have placed the protein 6 A above the HAP surface and there is
significant water above the protein in Z-direction. The box size is 141 x
146 x 125 A. I have got AMBER compatible parameters for HAP from a recently
published paper (the Interface force field).
I am facing similar problem as reported several years ago in amber mailing
list.
http://archive.ambermd.org/201106/0514.html
I am trying to minimise the system keeping the HAP rigid. Here is my input
script
System minimization:
&cntrl
imin=1, ntmin=1, nmropt=0,
maxcyc=2000, ncyc=1500,
ntx=1, irest=0,
ntpr=100, ntwr=100, iwrap=0,
ntf=1, ntb=1, es_cutoff=9.0, vdw_cutoff=11.0,
ntr=1, restraintmask=':HAA,HAB,HAC', restraint_wt=500,
/
There is some issue with the energies in particular vDW
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.9642E+09 4.1580E+04 5.6744E+06 HA 3277
BOND = 585136.3558 ANGLE = 319433.4389 DIHED =
2572.6253
VDWAALS = ************* EEL = -5610131.6247 HBOND =
0.0000
1-4 VDW = 1839.8371 1-4 EEL = 11004.4573 RESTRAINT =
0.0000
When I visualise the .rst file after minimisation, it seems that the HAP
surface is significantly changed as compared to the initial input. My
situation is very similar to the pics posted by Marek in 2010 to amber
mailing list
http://archive.ambermd.org/201008/0070.html
I would appreciate help regarding running the simulations of HAP in AMBER.
Thank you,
Neha
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Received on Mon Aug 15 2016 - 00:30:03 PDT
