[Chimera-users] Atom does not have a type
meng at cgl.ucsf.edu
Wed Oct 24 09:58:13 PDT 2007
It is my understanding that charges for all of those amino acid
residues should just be looked up in our AMBER charge table and not
calculated with Antechamber. I don't know what format issue is
causing the behavior.
We do have an "introduction to PDB format" in the Chimera manual,
and of course the PDB itself has a much longer and more detailed
explanation, but maybe if we take a look at the input PDB the problem
would be obvious.
Does Eric have your input PDB file? If not, you could send it to him
or to me privately (not to chimera-users) and we would try to take a
look. Things are quite busy now, so it might not happen right away.
Also, I will share the log that you just sent me, which will help.
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Oct 24, 2007, at 9:47 AM, Francesco Pietra wrote:
> Yes, I need the mol2 file for the scoring grid, though I also
> wanted what I thought to be a fixed pdb, may be for amber_scoring,
> or Amber MD. While I'll try to do better on the basis of your
> observations, I am attaching the log file, should it help the
> I was quite surprised by the query on total charges, suspecting
> that it arose from some fault doing from my side.
> Is it a documentation of the pdb format adopted by Chimera? In an
> attempt to discover non adherence to the pdb format (if that does
> not emerge from attached the error log), that would help me.
> Antechamber found no problems with the ligands, though big and
> ----- Original Message ----
> From: Elaine Meng <meng at cgl.ucsf.edu>
> To: Francesco Pietra <chiendarret at yahoo.com>
> Cc: chimera BB <chimera-users at cgl.ucsf.edu>
> Sent: Wednesday, October 24, 2007 6:19:26 PM
> Subject: Re: [Chimera-users] Atom does not have a type
> Hi Francesco,
> I don't know the details of your structure, but here are a few
> thoughts. There must still be atom name errors or missing atoms,
> because you are getting nonintegral charges.
> > On saving mol2, 1 model(s) had non-integral charge. I loaded this
> > mol2 file to
> > Chimera and saved as pdb.
> - Do not save Mol2 format and then read it in and write out again as
> PDB if you want PDB format. If you save Mol2 with SYBYL atom names,
> for example, you will have the wrong names when you change it into
> PDB format. Maybe that is part of the problem. The reason Dock Prep
> has the option to save Mol2 is that you may need this format to
> calculate the scoring grid for DOCK. If you want PDB format, just
> save PDB format after using Dock Prep (File.... Save PDB).
> > (I was unable to command the
> > visualization in Chimera of a particular residue, say THR 444.
> > Command :THR:444
> > returned all THR.
> - to specify just residue 444, don't say THR... for example
> display :444 means display residue 444
> display :444.x means display residue 444 in chain X only
> display :thr means display all THR
> display :thr:444 means display all THR and also residue 444
> > (6) Running Dock-Prep (all selected, except "Delete non-complexed
> > ions"; also
> > consider H-bonds; residue name HID specified.
> > A query was presented (in SYBYL naming) that I did not find where
> > to get help
> > about; therefore, I accepted the charge settings as it was
> > ASH + ALA + ASN +0
> > ASH + ALA + PRO +0
> > ASH + GLY + MET +0
> > GLH + ARG + LEU (w/HE2-1) +1
> > GLH + ARG + LEU (wo/HE2-1) +0
> > GLH + ARG + THR (w/1H-3) (wo/OXT-3) +1
> > GLH + ARG + THR (w/OXT-3) (wo/1H-3) +0
> - I don't understand what you mean here by SYBYL naming or these
> charges. Shouldn't GLH, LEU, and THR always be 0 (except at the
> termini, as you said) and ARG always be +1? Also, it should not be
> asking you about the charges for standard residues. There must be
> some naming or formatting error that causes the program to think
> these are nonstandard residues.
> For the residues with nonintegral charges, there should be messages
> about which atoms are not recognized, or if there are no such
> messages, they must be missing some of their atoms.
> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
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