AMBER Archive (2006)

Subject: Re: AMBER: MD with restraint (nmropt=1)

From: a a (patd_2_at_hotmail.com)
Date: Wed Dec 06 2006 - 00:11:59 CST

Dear Prof. Case,

I tried it several times and make the corrections as follows, however, i
don't know if I have misunderstand your answers, i still did not get it
works. Please kindly let me know how to get this tyoe of caluclations
done?

Input file:
Initial MD equilibration
&cntrl
  imin=0, irest=0,
  nstlim=2000, dt=0.001, ntc=1,
  ntpr=20, ntwx=20,
  cut=16, ntb=0, igb=1,
  ntt=3, gamma_ln=1.0,
  tempi=0.0, temp0=300.0,
/
&wt type = "END"&end
DISANG=./DISANG.rst

DISANG.rst file:
# distance restraints
&rst iat=-1, iresid=1, 4
IALTD=1
    r2=2.0, r3=5.0, r4=10.0
    igr1 = 1,4
GRNAM1(1)=O4
GRNAM1(4)=H61
&end
&rst iat=-1, iresid=1, 4
IALTD=1
    r2=2.0, r3=5.0, r4=10.0
    igr1 = 1,4
GRNAM1(1)=H3
GRNAM1(4)=N1
&end
&rst iat=-1, iresid=1, 4
IALTD=1
    r2=2.0, r3=5.0, r4=10.0
    igr1 = 1,4
GRNAM1(1)=O2
GRNAM1(4)=H2
&end
&rst iat=-1, iresid=2, 3
IALTD=1
    r2=2.0, r3=5.0, r4=10.0
    igr1 = 2,3,
GRNAM1(2)=O6
GRNAM1(3)=H41
&end
&rst iat=-1, iresid=2, 3
IALTD=1
    r2=2.0, r3=5.0, r4=10.0
    igr1 = 2,3
GRNAM1(2)=H1
GRNAM1(3)=N3
&end

What can I do next to solve this problem? Sorry to bother you again!

Best regards,

Annie

>From: "David A. Case" <case_at_scripps.edu>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: MD with restraint (nmropt=1)
>Date: Tue, 5 Dec 2006 13:24:37 -0800
>
>On Tue, Dec 05, 2006, a a wrote:
> >
> > I could like to run a minization and MD calculation with six hydrogen
>bond
> > restrainted. they are
> >
> > (residue 4, atomname H61)........(residue 1, atomname O4)
> > (residue 4, atomname N1)...........(residue 1, atomname H3)
> > (residue 4, atomname H2)...........(residue 1, atomname O2)
> > (residue 3, atomname H41).........(rsidue 2, atomname O6)
> > (residue 3, atomname N3)...........(residue 2, atomname H1)
> > (residue 3, atomname O2)............(residue 2, atomname H21)
>
>Each restraint needs to be in its own &rst namelist. Also note that atom
>names
>are case sensitive, "h3" is not the same as "H3".
>
>....dac
>
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