If you have your prmtop file, analyze it with rdparm and have it print out
the charges:
rdparm my.prmtop
And it'll bring up a prompt after listing the residues present.
Type "printAtoms", and it will print every atom with its number: name charge
mass (residue number:residue name) atom type and tree classification(?).
This should help show you where your problem is.
Good luck!
Jason
On Tue, Dec 14, 2010 at 8:29 AM, Rossella Noschese <
noschese.rossella.gmail.com> wrote:
> dear dr. Case,
>
> I made my model as I told you (modifying an hydrogen of ACE as to be a
> carbon), and it's ok, I set the atom type as CT and charge as 0.0000. I
> used
> the bond command, I manually erased the hydrogens on the carbons of this
> bond (I thought they would be erased by default with the command bond, but
> it wasn't so). However, I obtained my cyclic peptide. Pdb looks good. When
> I
> calculate the net charge, it gives me a charge of -0.21 (the sum of the
> charges of the hydrogen i erased on NME after binding and the hydrogen I
> transformed in C on ACE whose charge I turned in 0.0000).
> What about it?
> Thanks.
>
>
>
>
>
>
> 2010/12/9 case <case.biomaps.rutgers.edu>
>
> > On Thu, Dec 09, 2010, Rossella Noschese wrote:
> >
> > > Sorry if I was unclear. What I meant is something like this:
> > >
> > > X - (N)PRO-CO-CH2-CH2-CH2-NH-(C)PHE-X
> > > |
> |
> > > X - X - X - X - X - X
> > >
> > > with NPRO and CPHE i meant that CO and NH in the semplification above
> are
> > > not respectively those of PRO and PHE.
> > >
> > > .Dr Case: what I did using ACE and NME and then changing an hydrogen of
> > ACE
> > > mehyl group to a carbon isn't similar of drawning CO-CH2-CH2-CH2-NH ? I
> > > thought I only had to use then the command "bond". What about it?
> >
> > Sounds OK to me. I think I misunderstood what direction the peptide
> chain
> > was going earlier. Another way of
> > thinking about this is that you have a modified amino acid residue:
> > NH-CH2-CH2-CH2-CO. If this is correct(?) you have only amide
> connections,
> > no ketones or amines (as Francois seems to think). There are tutorials
> > (both
> > for R.E.D. and for antechamber) that walk through the construction of a
> > force
> > field for modified amino acid residues. If you called this modified
> > residue
> > "GAM" (for gamma-amino-acid), then your peptide sequence would be:
> >
> > GAM-PRO-X-X-...PHE
> >
> > and you would then add a bond between the C atom of PHE and the N atom of
> > GAM,
> > giving the structure you want.
> >
> > ....good luck....dac
> >
> >
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> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Dec 14 2010 - 07:00:02 PST
