AMBER Archive (2005)

Subject: Re: AMBER: the restraint MD fail with amber8,but success with amber7

From: Shulin Zhuang (shulin.zhuang_at_gmail.com)
Date: Fri May 13 2005 - 06:19:20 CDT

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_at_gmail.com
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