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 - 10:28:30 CDT

Dear Dr. Simmerling,

Thanks for your comments. I have done some tests with implicit solvent. All results seem to be reasonable. The explicit solvent calculation also looks OK.

Could you please list some ways to check the behavior of these restraints?

Thanks a lot,
Shaowen

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf Of Carlos Simmerling
Sent: Monday, April 20, 2009 10:13 AM
To: AMBER Mailing List
Subject: Re: [AMBER] help- regarding - TMD

I would be very careful with this setup to make sure everything is ok.
you have combined Cartesian positional restraints, NMR restraints (not
sure what they are since it is your disang file), and tgtmd
restraints.
you should check the behavior of each of these in your data.
they can in principle work together, but it is not obvious how to
design the restraints to work together, the code may not have been
well tested for the combination, and there is also possibility for
restraint conflicts.

On Mon, Apr 20, 2009 at 11:05 AM, Hu, Shaowen (JSC-SK)[Universities
Space Research Association USRA]. <shaowen.hu-1_at_nasa.gov> wrote:
> 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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