On Mon, Nov 28, 2005, Ananda Rama Krishnan Selvaraj wrote:
>
> To prepare the cluster input file in AMBER7, i have used the following
> commands in Xleap,
>
> (1) first way
>
> 1. xleap
> 2. source leaprc.gaff
> 3. loadAmberPrep prep.in file name of monomer
> 4. edit res name
> 5. saveoff res name res name.lib
> 6. loadoff res name.lib
> 7. frcmod = loadamberparams frcmod
> 8. x = loadpdb pdb-file name of the cluster
> 9. saveAmberParm x prmtop prmcrd
> 10. quit
>
> (2) second way
>
> 1. xleap
> 2. source leaprc.gaff
> 3. mods = loadamberparams frcmod
> 4. loadAmberPrep prep.in file name of the monomer
> 5. resseq = { resname, ........n-resname } ( n-number of monomers)
> 6. x = loadPdbUsingSeq pdb file name of the cluster resseq
> 7. saveAmberParm x prmtop prmcrd
> 8. quit
>
> In both ways, in the co-ordinate files the volume of the box is same by
> AMBER7.
> But the co-ordinate files from AMBER5 has lower volume than in AMBER7.
I am confused: neither of your examples sets up a periodic simulation, as far
as I can see. What exactly do you mean by the "volume of the box" being
different? In both of your examples, the coordinates in the prmcrd file
should just be whatever was in the pdb file that you loaded: LEaP is not doing
anything with these coordinates.
....dac
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Received on Mon Nov 28 2005 - 19:53:00 PST
