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 - 11:00:05 PST
