AMBER Archive (2004)

Subject: Re: AMBER: Angle restraint during MD

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Wed Jul 14 2004 - 08:39:38 CDT

sorry, that was a typo. check page 119.
  ----- Original Message -----
  From: Jiten
  To: amber_at_scripps.edu
  Sent: Wednesday, July 14, 2004 1:51 AM
  Subject: Re: AMBER: Angle restraint during MD

  Hello Dr. Carlos,

  In page 199 is about the analysis (ptraj). Also I do not want to use ntr (cartitian restraint) because it will forbid the translational and rotational motion of the ion.

  Regards,

  jiten
    ----- Original Message -----
    From: Carlos Simmerling
    To: amber_at_scripps.edu
    Sent: Wednesday, July 14, 2004 2:47 AM
    Subject: Re: AMBER: Angle restraint during MD

    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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