From: FyD <fy...@q4...> - 2008-10-30 12:46:21
|
Dear Bob, > The bad news: Looks like we have a file format issue here. Angel has it > right, that the mol2 format as specified uses SYBYL atom types. The AMBER > team has co-opted that file format for their own purposes, still calling it > "mol2" but using non-SYBYL atom types. Jmol expects a mol2 file to have mol2 > format. Openbabel does the same ;-) > The good news: Jmol is very flexible, and we have a rapid development cycle. > So we should be able to get it to do just about anything anyone wants it to > do. I'd particularly like to see the AMBER community embrace Jmol as an > alternative visualization tool. So let's get this working for you. > > The solution: For example, the AMBER, GAFF atom type list is small. Perhaps > we could have the mol2 reader map that list to element symbols. All this > would be easier if there were some identifying characteristic within the > mol2 file that clearly identified it as not being "true" mol2 format. But we > can work with just about anything. AMBER force fields (not only one force field but parm94, parm96, parm98, parm99, ff03 etc...) for proteins/nucleic acids use capital letters such CT, H1, H2, H3 etc... GLYCAM force field uses the same force field atom type definition as AMBER FF. GAFF force field uses small letters suc as c3, h1, h2 etc.. CHARMM force fields use other rules Why not simply taking the column of the FF atom types available in the Tripos mol2 file format & display it "as it is" ? -> If there are Sybyl force field atom types ( C.3, H, S.o, O.2, etc...), let's display them. -> If there are only chemical symbols, just display chemical symbols. -> If there are CHARMM, GLYCAM or GAFF force field atom types just display them as they are. best regards, Francois > On Thu, Oct 30, 2008 at 5:15 AM, Angel Herraez <ang...@ua...> wrote: > >> OK, I've got it >> >> Jmol is not using the atom name for element identification; mol2 has >> an "atom type" field which seems to be both the cause and the cure. >> http://www.tripos.com/data/support/mol2.pdf >> >> In your DMSO file, the atom type for the offending atoms is CT and >> H1. >> >> This is not supported by mol2 spec. See >> http://www.tripos.com/mol2/atom_types.html >> http://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom_types.html >> >> If you cahnge that to just C and H, Jmol behaves. You should maybe >> use the proper types, which seem to be C.3, H, S.o, O.2 >> They also work in Jmol. >> >> > > I guess it is because the name of >> > > the atoms are the following: C1 H11 H12 H13 S O C2 H21 H22 H23 >> >> As I said, not that name, but the type at column 50. |