AMBER Archive (2004)

Subject: Re: AMBER: Angle restraint during MD

From: Jiten (jiten_at_postech.ac.kr)
Date: Tue Jul 13 2004 - 11:21:28 CDT

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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