On Fri, Dec 14, 2012 at 2:38 AM, Indrajit Deb <biky2004indra.gmail.com>wrote:
> Dear amber users,
>
> Is it ok with the following script for tleap to use the parameter files
> developed by Santa Lucia Group with FF99CHI force field developed by
> Yildirim et al. ?
>
Does your script work? Does it give you what you want? If yes to both,
then yes, your script is OK. If no to either, then no, your script is not
OK.
You will get more useful answers with more specific questions. It's not
worthwhile to comb through a script we can't execute to see if we can find
any mistakes (e.g., a computer will find the typo 'loadpbd' faster than we
will, if we do at all) -- tleap can do that faster than us. Since we don't
have your files, we have no way of knowing whether you've forgotten
anything (were there any linkages, like disulfide bonds if you have protein
residues, is your system actually positively charged so you should have
added Cl- ions, do you have any custom residues you need to separately load
parameter files and library files for, etc.)
tleap will not fail quietly. If you've done something 'wrong', most likely
you will get a host of error messages (all of which you can google at this
point to find suitable solutions for, most likely). If a topology file is
written successfully, I suggest loading the resulting files into a
visualization program (e.g., VMD) and taking a look at the structure to
make sure it seems sensible.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Dec 14 2012 - 05:00:02 PST
