On Wed, Feb 01, 2012, Алексей Раевский wrote:
>
> tleap -s -f leaprc.ff99SB
>
> RC5 = loadmol2 rc5.mol2
.... (unnecessary(?) "set" commands...)
> NVA = loadmol2 nvach_red.mol2
>
> RRRN = sequence { RC5 RC RA NVA }
> savemol2 RRRN rrrn.mol2 1
> saveamberparm RRRN rrrn.prmtop rrrn.prmcrd
>
> And when I looked at rrrn.mol2 model in the viewer I saw that its
> coordinates are absoluetly different from the initial structure!
This is to be expected. There is no way the "sequence" command could know
anything about the structure of your molecule. If you have an initial
structure that you like, would would generally use the "loadPdb" command to
create the molecule (not the "sequence" command).
...hope this helps....dac
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Received on Wed Feb 01 2012 - 06:00:03 PST
