AMBER Archive (2009)

Subject: RE: [AMBER] help- regarding - TMD

From: Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (shaowen.hu-1_at_nasa.gov)
Date: Mon Apr 20 2009 - 10:05:38 CDT


Hi balaji,

I just got some results for my system with explicit water. Here is my input file:

 &cntrl
        imin = 0, ntx = 1, nstlim = 1000000,
        dt = 0.001, ntc = 2, ntf = 2, tol = 0.000001,
        tempi = 300.0, temp0 = 300.0,
        scee = 1.2, cut = 9.0,
        ntpr = 50, ntwx = 500, ntwr = 500,
        ntt = 3, gamma_ln = 1.0,
        ntb = 2, pres0 = 1.0, ntp = 1,
        taup = 2.0,
        nscm = 0, nmropt = 1, ntr = 1,
  restraint_wt=1.0,
  restraintmask=':67-251,259-467_at_CA,C,N',
        itgtmd = 1, tgtrmsd = 66.8998, tgtmdfrc = 0.1,
        tgtrmsmask=":1-28",
 /
 &wt
        TYPE='TGTRMSD', istep1=1, istep2=1000000,
        value1 = 66.8998, value2 = 0.0,
 /
 &wt
   type="END",
 /
LISTOUT=POUT
DISANG=../../../14d.rst

I used a restraint file for my ligand, which may not needed for you.

I am doing test. Hope somebody having experience can give some comments.

All the best,
Shaowen
________________________________________
From: amber-bounces_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of balaji nagarajan [balaji_sethu_at_hotmail.com]
Sent: Wednesday, April 15, 2009 10:19 AM
To: amber forumnew
Subject: [AMBER] help- regarding - TMD

Dear Amber ,

I am giving targeted molecular dynamics with explicit water

when i gave the following script
sander.MPI is running .
but when i see the out put file
tail -f tmdscript.out
its not printing any thing
I could not find our the error

help me out to solve this

the script as below
 &cntrl
  imin = 0,
  irest = 0 ,
  ntb = 2,
  ntxo = 1,
  ntx =1,
  tempi =300.0,
  ntc=2,
  ntr =0,
  ntf = 2,
  nscm = 100,
  ntwr = 100
  ntpr = 100,
  ntwx = 100,
  ntwv =100,
  ntwe = 100,
  ntt = 3,
  gamma_ln = 1.0,
  temp0 = 300.0
  nstlim = 2000000,
  dt = 0.002,
  cut = 10.0,
  itgtmd=1,
  tgtrmsd =0 ,
  tgtmdfrc =0.01,
  tgtfitmask= ":1- 76"
  tgtrmsmask= ":1- 76"

 /
regards
balaji
UOM

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