Dear Francois,
my problem is not that the RESP manual is not 100% correct - my problem is
that *respgen* produces RESP input that is not correct. Thus any procedure
that calls respgen, like e.g. residuegen will end up with charges that are
wrong. (This might be even if I derive the charges with RED and import them
with the -a flag, but this I haven't checked...)
So, bottom line: respgen produces an input according to the (old version of
the) manual, but this is simply not what resp expects as input.
All the best,
Th.
BTW: my problem with the naming is that RED wants the molecule file to be
named "Mol?_m?_s?*" or sth like this. Not a big issue, but it can be very
annoying (esp. as this is nowhere explicitly stated in the manual/tutorial -
well, at least I didn't see it there...).
Mit freundlichen Grüßen / Kind regards,
Dr. Thomas Fox
Boehringer Ingelheim Pharma GmbH & Co. KG
Dept. Lead Identific. and Optim. Sup. Ge
Tel.: +49 (7351) 54-7585
Fax: +49 (7351) 83-7585
mailto:thomas.fox.boehringer-ingelheim.com
Boehringer Ingelheim Pharma GmbH & Co. KG, Sitz: Ingelheim am Rhein;
Registergericht Mainz: HR A 22206; Komplementär Boehringer Ingelheim
Deutschland GmbH; Geschäftsführung: Dr. Engelbert Günster (Vorsitzender),
Ralf Gorniak, Mark Hagmann, Michael Klein, Dr. Martin Wanning; Vorsitzender
des Aufsichtsrates: Prof. Dr. Dr. Andreas Barner; Sitz: Ingelheim am Rhein;
Registergericht Mainz: HR B 23260
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-----Ursprüngliche Nachricht-----
Von: FyD [mailto:fyd.q4md-forcefieldtools.org]
Gesendet: Freitag, 23. September 2011 16:27
An: AMBER Mailing List
Betreff: Re: [AMBER] bug in respgen ?
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
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Received on Mon Sep 26 2011 - 00:30:02 PDT
