David hello!
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 )
After this I've edit my structure ( edit m) and save it too.
Unfortunatelly the atom names in edit ACE group were like before editing 0)
Could you tell me how I can add new units- groups to the exiting param sets
without xleap graph interface ?
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.
Thanks again,
James
2011/11/10 David A Case <case.biomaps.rutgers.edu>
> On Thu, Nov 10, 2011, James Starlight wrote:
> >
> > 1- I've edit my reference by means of the param10 set. Before editing of
> my
> > structure also I've edit some properties of ACE group ( I just rename
> atoms
> > in that groups) but after saving my structure the names of atoms in ACE
> > group were still unchanged. How I can rename atoms in different
> functional
> > groups forever ? :)
>
> This is not specific enough information. We need to know exactly what
> sequence of commands you used to edit the atom names, what commands were
> used
> to "save the structure", what you did to conclude that the atoms names were
> unchanged.
>
> [As an aside, why would you want to change the atom names of standard
> residues? That is almost certainly going to lead to grief later on.]
>
> >
> > 2- My initial structure consisted of 2 identical alpha helices but after
> > saving both of monomers were merged into one chain ( so from started pdb
> > the string about chains A and B was deleted ). How to prevent this
> > merging ? I want that my output structure will consist of 2 chains as an
> > input one.
>
> Put a TER card in the input pdb file between the two chains.
>
> ....dac
>
>
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Received on Thu Nov 10 2011 - 11:00:03 PST
