Elaine: 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. Thanks francesco ----- Original Message ---- From: Elaine Meng <meng@cgl.ucsf.edu> To: Francesco Pietra <chiendarret@yahoo.com> Cc: chimera BB <chimera-users@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 ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com