Hi,
> But this may be a problem when you are disappearing, say, one residue in a
> stretch of RNA, since then you will end up with two separate pieces of
> RNA.
but, if you are removing an RNA base in the middle of a strand, you do
want to end up with two separate pieces of DNA, dont you? Removing one
base and subsequently closing the gap would be two big changes to simulate
at once and I am not sure if a typical TI calculation would converge well
on this. You could do it by deleting residue n in v1 and adding a (very
long) bond between residues n-1 and n+1 at the appropriate place in leap.
This transformation sounds like horribly difficult sampling to me, though.
> So, I am wondering, is it possible to do in the VDW step what one usually
> does for the charge, i.e,
>
> crgmask_v0=:10
> scmask_v0=''
> crgmask_v1=:10
> scmask_v1=:10
>
> while using the same prm and rst file for both V0 and V1? (in V0 you have
> a
> residue 10 without charge but with VDW, while in V1 you have residue 10
> without charge and without VDW).
No, you cant set things up this way. The syntax you describe would make
sense for disappearing residues, but that is not how the current code
works.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Tue Mar 19 2013 - 04:30:03 PDT
