[Chimera-users] Atom does not have a type

Francesco Pietra chiendarret at yahoo.com
Wed Oct 24 09:47:04 PDT 2007


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 diagnosis.

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 complicated.


----- 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 presented:
> 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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