AMBER Archive (2004)

Subject: Re: AMBER: Angle restraint during MD

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Tue Jul 13 2004 - 12:47:16 CDT

try reading the section starting at page 199 too, it tells you
there how to use the iat() values for angle restraints.

  ----- Original Message -----
  From: Jiten
  To: amber_at_scripps.edu
  Sent: Tuesday, July 13, 2004 12:21 PM
  Subject: Re: AMBER: Angle restraint during MD

  Hello Dr. Carlos,

  What I can see in the amber8 manual (5.20.3 - page 162) about the makeANG_RST is about defining only the tortional restraints. So, it seems to me that for the angle restraint between three atoms (A-B-C) - I should rather define the distance restraint between A and C. Am I right? If not how can what could be the format of contraint and constraint_library ?

  I tried to a perform constant volume (few tortional restraint ) MD from the restart file generated again from contant volume minimization with few tortional restraints. (FOr testing recently installed amber8 in Opteron)

  For minimization

   &cntrl
      imin=1, maxcyc=2000, ncyc=1000, nmropt=1,
      cut=6.0,
      ipol=1,
      ntpr=10, ntb=1,
   &wt type='END' /

  LISTOUT=POUT_dmso_min
  DISANG=RST_Tri_cons

  Upto here no problem . Then for the constant volume MD

  &cntrl
   imin=0, irest=0, ntx=1, tempi=0.0, cut=11.0,
   ntt=1, temp0=300.0, tautp=2.0, nmropt=1,
   ntp=0, nrespa=1, ipol=1,
   ntb=1, ntc=1, ntf=1,
   nstlim=100000, dt=0.001,
   ntwe=200, ntwx=200, ntpr=200,
  &wt type='END' /

  LISTOUT=POUT_dmso_cv
  DISANG=RST_Tri_cons

  --- I find in the output file that

   Here is the input file:

  &cntrl
   imin=0, irest=0, ntx=1, tempi=0.0, cut=11.0,
   ntt=1, temp0=300.0, tautp=2.0, nmropt=1,
   ntp=0, nrespa=1, ipol=1,
   ntb=1, ntc=1, ntf=1,
   nstlim=100000, dt=0.001,
   ntwe=200, ntwx=200, ntpr=200,
  &wt type='END' /

  LISTOUT=POUT_dmso_cv
  DISANG=RST_Tri_cons

   Could not find cntrl namelist

  I check each of the cntrl keys in amber8 manual. Each of them are there as well. I am wondering where could be the error.

  With regards,

  Jiten

    ----- Original Message -----
    From: Carlos Simmerling
    To: amber_at_scripps.edu
    Sent: Tuesday, July 13, 2004 9:00 PM
    Subject: Re: AMBER: Angle restraint during MD

    ok, I didn't understand the last mail well. you can
    definitely do angle restraints using the NMR restraint
    option. check the manual carefully, and if it is not clear,
    please let us know which part you do not understand.
      ----- Original Message -----
      From: Jiten
      To: amber_at_scripps.edu
      Sent: Tuesday, July 13, 2004 5:28 AM
      Subject: AMBER: Angle restraint during MD

      Hello all,

      Sorry for the previous mail without subject.

      Sander does no more support the restrainXYZ in the parmtop file. But using the NMR restraint I could do only distance and torsional angle restraint. I wish to put a small ion (having 3 atoms) under angle restraint during MD. I am wondering how can I solve this probelm

      Any suggestions will be highly appreciated.

      Thanks inadvance,

      N. Jiten Singh
      C/O Prof. Kwang S. Kim
      Department of Chemistry
      Pohang University of Science and Technology
      San 31, Hyojadong, Namgu
      Pohang 790-784, Korea
      Phone : 82-54-279-5853 ( Lab ) / 279-4138 ( Appt )
      Fax : 82-54-279-8137 (or +82-54-279-3399)
      Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e
      Home Page : http://www.geocities.com/njs_19

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