David,
I saved anything by means of Xleap context menu
E.g for saving pdb file after editing I've used File-> SavePDB than I've
chose my unit M and save edited.pdb file )
I have no problems with processed files exept chains merged in one )
James
2011/11/10 David A Case <case.biomaps.rutgers.edu>
> On Thu, Nov 10, 2011, James Starlight wrote:
> >
> > 1) I've load my pdb by the
> > source leaprc.ff10
> > m = loadpdb 1MAG_0.pdb
> > edit m
> >
> > I've edit ACE entry from the Xleap meny edit Unit- Ace ( I've rename
> atoms
> > and save addter this )
>
> Not sure what command use used to "save" the ACE group. If you do this:
>
> saveOff ACE my_ace.lib
>
> Then you should be able to look at my_ace.lib and see that the new atom
> names
> are there. If you later "loadOff my_ace.lib" you will get an ACE library
> with the new names.
>
> This won't change what is in "ff10": if you want those to change, you will
> need to change the ff10 library files. See
> $AMBERHOME/dat/leap/lib/ff10.cmd
> to see how those libraries were made in the first place. That might show
> you how to change them.
>
> > 2) I've made TER beetween chains but edited structure after this had
> > consisted of one chain where each residues were divided by the TER card
> ;O
> > But I want to obtain just 2 chains as a output as was in input :)
> > I've attached structure before and after editing.
>
> Again, without knowing the exact commands you used, it's very hard to
> figure
> out what is going on. When you say things like "I edited the structure and
> then saved it", you are telling us what you *intended* to do, but not what
> you
> actually did. (Take a look at your email above: you got started on the
> right
> direction by listing the actual input for the first three commands, but
> then stopped doing that for the rest of the email.)
>
> ...hope this helps...dac
>
>
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Received on Thu Nov 10 2011 - 12:00:02 PST
