Re: Re: AMBER: Sander: idecomp

From: Xiao He <hx.itcc.nju.edu.cn>
Date: Mon, 28 Mar 2005 21:44:53 +0800

Either Amber7 or Amber8 can do this.You can refer to Amber7's manual,since anal is retired in Amber8

Here is a example I did:
TITLE
 1 1 0 0 0 1
 0 1.0 1.0 1.0 90.0
 1 0 0 0 0 1
 20 2.0 2.0 1.0
 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
ENERGY
GROUP
RES 1
END
GROUP2
RES 2
END
END
END

command
anal [-O] -i analin -o analout -p prmtop -c inpcrd [-ref refc ]

Good luck!

He Xiao

Country: People's Republic of China
UniversityNanjing University
Department: Institute of Theoretical Computational Chemistry, College of Chemistry & Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE
DegreeSencond year for Master's Degree
Website:http://itcc.nju.edu.cn/

>Thanks, Jack. Does AMBER8 include this module or I have to use AMBER7?
>
>Lei
>
>Jack Lei wrote:
>
>> Anal could do it.
>>
>> Jack
>>
>> On Tue, 15 Mar 2005 14:45:47 -0500, lei jia <jial.broyde.nyu.edu> wrote:
>> > Dear Amber users,
>> >
>> > I am using MM-PBSA generated sander input file to calculate the
>> > component interactions of a group of atoms. I had no problem to
>> > calculate them on the residue level by using the RES card. I wonder if I
>> > can do that on the atom level by using the ATOM card in the group
>> > specification section. If not, what can I do to calculate the
>> > interactions between the whole molecule and several atoms belong to the
>> > molecule. Thanks a lot!
>> >
>> > Lei
>> >
>> > Here are my input files and error messages from the output:
>> > #############################################################
>> > File generated by mm_pbsa.pl. Using MM
>> > &cntrl
>> > ntf = 1, ntb = 0, dielc = 1,
>> > idecomp= 1,
>> > igb = 2, saltcon= 0,
>> > offset = 0.09, extdiel= 78.5,
>> > gbsa = 0, surften= 1.0,
>> > cut = 99999.0, nsnb = 99999,
>> > scnb = 2.0, scee = 1.2,
>> >
>> > imin = 1, maxcyc = 1, ncyc =0,
>> > &end
>> > Residues considered as REC
>> > RRES 1 22
>> > END
>> > Residues to print
>> > ATOM 173 182
>> > END
>> > END
>> > ######################################################
>> > ----- READING GROUP 2; TITLE:
>> > Residues to print
>> > ***PROBLEMS WITH GROUPATOM 173 182 0 0 0 0 0
>> > 0 0 0 0 0 0 0*******
>> >
>> > Number of atoms in this group = 0
>> >
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= = = = = = = = = = = = = = = = = = = =
                        

        崑

 
                                 
        Xiao He
        hx.itcc.nju.edu.cn
          2005-03-16



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