Thomas,
> thanks for pointing this out, and indeed I have downloaded and used the RED
> perl scripts to get charges. However, for a number of reasons (one of them is
> implementing the procedure into one of our
> modeling-work-horse-fancy-software-monoliths) I would rather have residuegen
> do the work for me. Another reason is that I found myself rather limited in
> the possibilities how I name my molecule files when using RED, but I don't
> want to dig through the whole perl code to change this...
The (iupac) name of a molecule is defined in the P2N file as it follows:
REMARK TITLE SET_OF_WORD_WITHOUT_ANY_SPACE_CHARACTER
> Yet another reason
> is that I have some non-amino acid covalent binders and not non-standard
> amino acids and there I wasn't sure how well RED can handle this (probably it
> can, but I haven't tried).
Yes, R.E.D. III.x handles non-amino acid covalent binders, obviously
non-standard residues (it was first designed for these), bio-inorganic
complexes as well as transition states.
R.E.D. Server/R.E.D. IV perform many tasks automatically...
> So I took a step back and got to the basics like
> residuegen, then respgen, and finally resp.
>
> So having seen Alex' post, it seems that there seems to be a definite problem
> in respgen - so I hope that maybe someone who is more into charge derivation
> (and has a better overview of the different scenarios how to use resp(gen) )
> can have a look and a good idea how to modify the code that it works for all
> the different cases (single mol single conf, single mol multi conf, multi
> mols...etc)
When intra/inter-molecular charge constraints are used and nmol=1
(i.e. a single conformation and a single orientation) it is reported
in the original RESP manual that one should jump a line but this is
not correct.
We have modified the RESP manual; see
http://q4md-forcefieldtools.org/RED/resp/ to underline this problem:
see *blank to end only if the number of structure(s) "nmol" is
different from 1
Is it the problem you report?
regards, Francois
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 23 2011 - 07:30:03 PDT
