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.scripps.edu>
>Reply-To: amber.scripps.edu
>To: amber.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
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
_________________________________________________________________
Learn English via Shopping Game, FREE!
http://www.linguaphonenet.com/BannerTrack.asp?EMSCode=MSN06-03ETFJ-0211E
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Dec 08 2006 - 16:22:52 PST
