Amber-style mol2 name
Hi all, Simple Questions: To create mol2 files with naming compatible with Ambersuite programs I would have to save with non-sybyl hydrogen naming, yes? Also, after I save the files with the amber style naming scheme, which atom name column has the AMBER style naming (there are two)? Thanks! Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion@syr.edu
Hi Nikolay, The columns are the atom *name* and the atom *type*. The one before the coordinates is the name. I don't know what you mean by "compatible," are you trying to use the Mol2 file as input to one of the Amber-suite programs? As you saw, there is an option in the Mol2 saving dialog to write Amber/GAFF types instead of SYBYL types. There is no option for Amber atom names. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#mol2> I don't know if the Mol2 file with Amber/GAFF types is intended as input to another program. It is not intended as input back into Chimera. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 24, 2012, at 9:42 AM, Nikolay Igorovich Rodionov wrote:
Hi all, Simple Questions: To create mol2 files with naming compatible with Ambersuite programs I would have to save with non-sybyl hydrogen naming, yes? Also, after I save the files with the amber style naming scheme, which atom name column has the AMBER style naming (there are two)? Thanks! Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015
I making a .gro gromacs input file that references data from the built in amber99sb.itp so the atom names need to match Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion@syr.edu On 10/24/12 12:55 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
the atom *name* and the atom *type*. The one before the coordi
Sorry, there is no option in Chimera to rename your atoms with Amber names. Looks like the PDB2PQR server might be able to do it: <http://nbcr-222.ucsd.edu/pdb2pqr_1.8/> I haven't tried it, though. If it works, you could read the resulting PQR into Chimera and then write Mol2. Elaine
Would you mind elaborating about the differences between atom types and atom names? I thought they were essential one in the same; looking at a generic mol2 file, it seems like every atom name has a unique atom type. What differentiates them? Thanks! Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion@syr.edu On 10/24/12 6:00 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Sorry, there is no option in Chimera to rename your atoms with Amber names. Looks like the PDB2PQR server might be able to do it:
<http://nbcr-222.ucsd.edu/pdb2pqr_1.8/>
I haven't tried it, though. If it works, you could read the resulting PQR into Chimera and then write Mol2. Elaine
Well, there are exceptions to everything, but generally: Atom types define what parameters are assigned to the atom in various calculations. Often there will be many atoms in a residue that have the same type, but they could have different names... For example, in this Mol2 file, every atom has a unique name, but all of the hydrogens are type H, two carbons are type C.2, and the remaining carbons are type C.3. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/example.mol2in> Some formats or programs require unique atom names in a residue so that each atom can be specified uniquely, but some do not have this requirement. Different programs have different atom-naming rules, and these atom names might or might not imply the types of the atoms. Different programs use different sets of types, and you have to look at the documentation for that program to see a description of the types. If you want more perspectives on these concepts, you could try asking on ccl.net. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 25, 2012, at 3:14 AM, Nikolay Igorovich Rodionov wrote:
Would you mind elaborating about the differences between atom types and atom names? I thought they were essential one in the same; looking at a generic mol2 file, it seems like every atom name has a unique atom type. What differentiates them?
Okay, that makes perfect sense, thanks!!! Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion@syr.edu On 10/25/12 11:52 AM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
ormats or programs require unique atom n
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