Thank you very much
The Amber version I used is Amber 8.
My input files is:
molecular dynamics run
&cntrl
nmropt=1, vlimit=20,
imin=0,irest=0,ntx=1,
tempi=0.0,temp0=300,tautp=1.0,
ntt=1,npscal=1,nsnb=25,
ntp=0,ntb=1,ntr=1,
ntc=2,ntf=2,scee=1.2,
nstlim=25000,dt=0.002,
ntwx=500,ntpr=25,ntwr=500,
cut=12.0,
&end
&wt
type='TEMP0',istep1=0,istep2=2500,
value1=0.0,value2=50.0,
&end
&wt
type='TEMP0',istep1=2500,istep2=5000,
value1=50.0,value2=100.0,
&end
&wt
type='TEMP0',istep1=5000,istep2=7500,
value1=100.0,value2=150.0,
&end
&wt
type='TEMP0',istep1=7500,istep2=10000,
value1=150.0,value2=200.0,
&end
&wt
type='TEMP0',istep1=10000,istep2=15000,
value1=200.0,value2=300.0,
&end
&wt
type='TEMP0',istep1=15000,istep2=25000,
value1=300.0,value2=300.0,
&end
&wt
type='END',
&end
&rst
iat=0,
&end
Restrain the Protein heavy atoms I
5.0
FIND
* C * *
* CA * *
* CB * *
* CC * *
* CD * *
* CE * *
* CG * *
* CZ * *
* CH * *
SEARCH
RES 1 350
END
Restrain the Protein heavy atoms II
5.0
FIND
* N * *
* NH * *
* ND * *
* NE * *
* NZ * *
* O * *
* OG * *
* OH * *
* OE * *
SEARCH
RES 1 350
END
Restrain the Protein heavy atoms III
5.0
FIND
* P * *
* SG * *
* O1P * *
* O2P * *
* O3P * *
SEARCH
RES 1 350
END
Restrain the peptide heavy atoms I
5.0
FIND
* C * *
* CA * *
* CB * *
* CC * *
* CD * *
* CE * *
* CG * *
* CZ * *
* CH * *
SEARCH
RES 351 368
END
Restrain the peptide heavy atoms II
5.0
FIND
* N * *
* NH * *
* ND * *
* NE * *
* NZ * *
* O * *
* OE * *
SEARCH
RES 351 368
END
END
After this procedure, I found the complex is almost identical with
my reference structure(leap.mdcrd, leap.pdb) without any changes, that
is to say, the complex wasn't affected any more in the course of
temprature raising. The 5kcal force was put on the heavy atoms exept H
atom.
thank you
--
Na Zhang
Chemistry Department
Zhejiang University PRC
xbcdnana.gmail.com
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Received on Mon Nov 21 2005 - 14:53:00 PST
