AMBER Archive (2009)

Subject: Re: [AMBER] implicit solvent simulation

From: Ashish Runthala (ashish.runthala_at_gmail.com)
Date: Thu Aug 06 2009 - 00:00:50 CDT

See the script is correct but check for the restraintmask format as it
is different in different AMBER versions. And also check whether you
need to use the polarized state or not by using ipol=1, and
saveamberparmpol.
See there are many runs like equilibration run and production run
instead of directly going to heating run. Just watch out what you are
attempting.

On Thu, Aug 6, 2009 at 1:49 PM, Manish Kumar<kumarmanish.amb_at_gmail.com> wrote:
> Dear Experts,
>
> I am doing implicit solvent simulation.
>
> My tleap commands were:
>
> tleap -s -f leaprc.ff99SB
> source leaprc.gaff
> loadAmberParams LIG.frcmod
> loadAmberPrep LIG_amber.prepc
> set default PBradii mbondi2
> com = loadpdb PROT_lig.pdb
> check com
> saveamberparm com cplx_wt_impli.prmtop cplx_wt_impli.inpcrd
>
>
> Minimization script is:
>
> &cntrl
> imin=1,maxcyc=2000,ncyc=1000,
> cut=999.0,
> igb=5,ntb=0,
> ntc=2,ntf=2,
> ntpr=100,
> ntr=1, restraintmask=':1-215',
> restraint_wt=50.0
>
> Heating Script is:
>
> &cntrl
> imin=0,irest=0,ntx=1,
> nstlim=100000,dt=0.001,
> ntc=2,ntf=2,
> cut=999.0,
> igb=5,ntb=0,
> ntpr=1000, ntwx=0,
> ntt=3, gamma_ln=2.0,
> tempi=0.0, temp0=300.0,
> ntr=1, restraintmask=':1-215',
> restraint_wt=5.0,
> nmropt=1
> /
> &wt TYPE='TEMP0', istep1=0, istep2=100000,
> value1=0.1, value2=300.0, /
> &wt TYPE='END' /
>
> I will be very thankful if someone can look over these scripts and assure
> me that these are correct.
>
> Manish
> _______________________________________________
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> AMBER_at_ambermd.org
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> 

-- 
Ashish Runthala,
Faculty Division III,
Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031
INDIA

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