Eric: Thanks. Please see below. --- Eric Pettersen <pett@cgl.ucsf.edu> wrote:
On Nov 23, 2007, at 12:56 PM, Francesco Pietra wrote:
Here I really don't understand. With your "including recent changes" above, I understand that you follow 3.0 or 3.1 PDB format. Unless you add that 3.0 and 3.1 formats are exercises not to follow (the official pdb booklet I have, is V. 2.3, added of V. 3.0 and V 3.1). If you follow 3.0, modification of Amber's file
As Elaine mentioned, v2.3 PDB files would place 'H' in column 14, so a 4-letter hydrogen name would be something like 1HD1, whereas in v3.0 they decided to just have the H start the name, producing names like HD11. The fact that Chimera still produces v2.3 hydrogen names is wrong, and I have added your name to the bug-database entry for producing 3.0 names, but nonetheless the PDB changeover to 3.0 only happened a few months back, so most programs should be able to handle both forms.
I succeed in letting LEaP (Amber9) reading pdb files written by Chimera. Which may still be in the economy in view of "delete overlapping residues" possibility in Chimera.
Finally, everything in the "classic" are is in view of MD. Even DOCK is recommended as a preliminary to MD (by both Scott Brozell and D case). Therefore, it is a pity - to say politely - having to spend so much effort in rectifying files from pre-programs. Unless Chimera is bound to some other MD suite than Amber, to which MD suite Chimera's files flow in without barriers.
Chimera isn't "bound" to any MD suite in particular. It simply tries to produce standard PDB files. The only software we've made a conscious attempt to coordinate with is DOCK.
Yes, and that is an extremely useful coordination. However, DOCK is strictly bound to Amber. I don't simply mean the DOCK's built-in amber_rescore, but Scott Brozell indication to run Amber's MD after the series of dockings. I can say again that in my opinion Chimera is a gem. I could not have done what I have done so far in docking-MD without Chimera. Now - with side help by VMD - I have the protein-ligand complex in a membrane, the whole solvated. Though, a choice of different protocols when saving pdb files from Chimera ("saving for LEaP) would speed up the work by certain users. Is it a major modification of software? Cheers francesco
--Eric
Eric Pettersen UCSF Computer Graphics Lab
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