Dear Simmerling,
Great appreciation for your answering my problem!
I also use constraint for the minimization and it runs well.
The whole input file is as follows:
molecular dynamics run
&cntrl
nmropt=1, vlimit=20
imin=0,irest=0,ntx=1,
tempi=0.0,temp0=300,tautp=0.5
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,
lastist = 3500000,lastrst = 5000000
&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
50.0
FIND
* C * *
* CA * *
* CB * *
* CC * *
* CD * *
* CK * *
* CM * *
* CN * *
* CQ * *
SEARCH
RES 1 342
END
Restrain the Protein heavy atoms II
50.0
FIND
* CR * *
* CT * *
* CV * *
* CW * *
* C* * *
* CY * *
* CZ * *
* N * *
* NA * *
SEARCH
RES 1 342
END
Restrain the Protein heavy atoms III
50.0
FIND
* NC * *
* N2 * *
* N3 * *
* NT * *
* N* * *
* NY * *
* NB * *
* O * *
* O2 * *
SEARCH
RES 1 342
END
Restrain the Protein heavy atoms III
50.0
FIND
* OH * *
* OS * *
* P * *
* S * *
* SH * *
SEARCH
RES 1 342
END
Restrain the lig heavy atoms I
50.0
FIND
* ca * *
* c * *
* ce * *
* c3 * *
* n2 * *
* o * *
* os * *
* oh * *
SEARCH
RES 343
END
END
--
Shulin Zhuang
Chemistry Department
Zhejiang University PRC
shulin.zhuang.gmail.com
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Received on Fri May 13 2005 - 12:53:00 PDT
