AMBER Archive (2004)

Subject: Re: AMBER: Angle restraint during MD and namelist problem in amber8

From: Jiten (jiten_at_postech.ac.kr)
Date: Wed Jul 14 2004 - 11:13:38 CDT

Dear Dr. Carlos,

Thanks for your suggestions. In one of my previous mail Imention about namelist proplem with amber8 (though it works without any problem with amber7) - Again I include the same. 

---
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: Wednesday, July 14, 2004 10:39 PM
  Subject: Re: AMBER: Angle restraint during MD

  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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