From: Shirley Li (li19104_at_yahoo.com)
Date: Tue Dec 27 2005 - 12:38:15 CST
Hi Peter,
Thanks a lot for your response and confirmation.
Best regards,
Shirley
Peter Freddolino <petefred_at_ks.uiuc.edu> wrote: Shirley,
this is correct if you need uncharged termini. If you do not insert
first/last statements, it will automatically add a standard charged N
and C terminus.
Best,
Peter
Shirley Li wrote:
> Hi Peter,
>
> Regarding psfgen, is it necessary to add ACE/CT3 to the two termini,
> i.e., to generate individual segment with:
>
> segment A {
> pdb chainA.pdb
> first ACE
> last CT3
> }
> instead of:
> segment A {pdb chainA.pdb}?
>
> Thank you.
>
> Shirley
>
>
> */Peter Freddolino
/* wrote:
>
> Hi Irene,
> the similar numbering by itself should not be a problem. However,
> if you
> have multiple chains, you need to feed them in to psfgen as two
> separate
> files for it to properly generate the proteins and (especially) the
> terminii. If you do not do that, chances are that their
> connectivity has
> them joined end to end. You should probably split the chains into two
> pdb files, and then in psfgen do something like
> segment A {pdb chainA.pdb}
> segment B {pdb chainB.pdb}
> coordpdb chainA.pdb A
> coordpdb chainB.pdb B
>
> Does this make sense? The chain field by itself does not make a
> difference. Counterions are also very important, so you should add
> these
> using autoionize in vmd.
>
> Best,
> Peter
>
> Irene Newhouse wrote:
>
> > We have a dimer protein we're working with, and we're wondering
> > whether psfgen can cope with having the corresponding residues
> in both
> > monomers having the same resid , or do we have to renumber the 2nd
> > monomer?
> >
> > The pdb file from which we start [built by genomics types from an
> > homology model] starts with residue 26. Could that be a problem? At
> > the very right of each line is a field CHA for every atom in
> monomer
> > 1 & CHB inr monomer 2, but the field right after the atom type,
> which
> > should contain A or B is empty. [That matters to some viewers].
> > Should I populate it with As & Bs as appropriate, or doesn't it
> matter
> > to psfgen?
> >
> > [We thought we'd gotten through the process with the initial pdb
> file
> > as is, but the protein sort of uncoils during MD. The other thing
> > that's different from our previous projects is that this protein
> has
> > a lot of charged residues, so needs to have counterions added.
> We're
> > trying to figure out where things went wrong & these two
> differences
> > are our current focus].
> >
> > Thanks!
> > Irene Newhouse
> > U. of Hawaii
> >
>
>
> ------------------------------------------------------------------------
> Yahoo! for Good - Make a difference this year.
>
---------------------------------
Yahoo! Shopping
Find Great Deals on Holiday Gifts at Yahoo! Shopping
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:28 CST