Howdy all,
I've been playing with trying to convert CHARMM force field files... I
want to be able to run some of the CHARMM force fields directly in AMBER
since I find CHARMM difficult. The idea is to generate AMBER compatible
format, but I am running into a few little hiccups so I thought I'd ask
the "list" and see if people have any better ideas or suggestions for
refocusing my efforts... Specifically:
- should I focus instead on modifying LEaP to read the CHARMM files directly?
- should I instead finish the Crowley converters?
- should I generate PLEP, LEaP off, or mol2 or possibly develop a new
generic format which would allow conversion from any force field?
Original plan: Perl script to read .rtf and .prm files and convert these
to PREP and parmXX.dat formats which could be loaded into LEaP. After two
days progress was modest except I got stuck on the IC (internal coordinate
format) in CHARMM and the corresponding PREP internal coordinate table.
It gets tricky due to the need to specify loop closure bonds and to handle
the extra information in CHARMM (i.e. connections to previous and next
residues and virtual impropers used for coordinate generation). I also am
not fully versed in the CHARMM IC representation (although I guess I could
go in the CHARMM source).
Then I thought, why not simply dump the cartesian coordinates; if I do
this, I can avoid all the chain identifiers and ignore the CHARMM IC
table. Easiest along these lines is to simply use the mol2 format.
Better may be to use PREP format (as I could infer the chains).
To get the coordinate information, I (can) supply a PDB file that has
coordinates for every residue (unpatched). I can parse this and the
RTF/PRM files to create separate .mol2 files for every residue (and every
possible patch). These can be loaded up into LEaP, however information is
missing in the mol2 format such as the connectivity (to previous/next
residues). [I could grab this info and use it to create a leaprc file
that does the appropriate specification.] Right now I am hitting an issue
that LEaP doesn't recognize the loaded mol2 molecule.
Eventually I will have to dig into LEaP to enable funny terms (CMAP,
NBFIX, ...).
Ideas? Also, can someone remind me of the status of the Scripps
converters or what not that were being worked on? ...and also remind me
why I might not want to use mol2 format.
...and finally, can someone remind me what LEaP does or does not do with
the impropers? If I remember correctly, LEaP ignores the impropers in the
PREP file and magically generates its own? If this is still the case,
I'll have to dig into LEaP to disable the improper generation.
thanks,
--tom
Received on Sun Oct 08 2006 - 06:07:33 PDT
