Quoting Shozeb Haider <shozeb.haider.pharmacy.ac.uk>:
>
> I am trying to simulate a modified pentapeptide. On running antechamber
> the -rn flag labels the entire pentapeptide as single unit (MOL
> default). When I then load it in xleap and set up the system it is only
> recognised as one long molecule. In other words, the peptides do not
> retain their name labels. Is there some way one can prevent antechamber
> from adding in the name label ? or allow it to use the original labels.
Usually when you derive charges you do it for a _small_ molecule. This
small molecule is usually a single residue to build a force field
library for this small molecule (or a fragment built from this small
molecule).
That being said, you can use R.E.D. where the final output is the
Tripos mol2 file format, and where multiple residue naming
http://q4md-forcefieldtools.org/RED/ is fully handled.
See for instance the "W-59" R.E.DD.B. project with the corresponding
Tripos mol2 file available:
http://q4md-forcefieldtools.org/REDDB/up/W-59/tripos1.mol2
regards, Francois
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Received on Sun Jan 13 2008 - 06:07:21 PST
