Dear Thomas,
> my problem is not that the RESP manual is not 100% correct - my problem is
> that *respgen* produces RESP input that is not correct.
Yes, I got it ;-) but it looks like the Antechamber developers
followed the error in the old RESP manual. This is a reason - among
others - why we have updated the RESP manual .
http://q4md-forcefieldtools.org/RED/resp/
> Thus any procedure
> that calls respgen, like e.g. residuegen will end up with charges that are
> wrong.
If there is no intra-molecular charge constraint and no
inter-molecular charge constraint the charge values should be correct;
i.e. they remain _correct_ for a _whole_ molecule, and they are wrong
(if I understand you) for a molecular fragment when the number of
conformation/orientation equals one.
> (This might be even if I derive the charges with RED and import them
> with the -a flag, but this I haven't checked...)
R.E.D. is based on this new RESP manual version, and directly generate
mol2 files from the RESP output. We do not use Antechamber.
> 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.
ok, I will run jobs with R.E.D. Server & send you the corresponding
web addresses with nmol = 1 and nmol = 2 (resp input correspondence)
with intra-molecular charge constraints. Give me 10 minutes.
> 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...).
Mol_m1-o1.mol2
m1 means molecule number $n = 1
o1 means optimized geometry i.e. conformation number $i = 1
(in MEP computation $j means number of orientations)
Mol_m1-o1-sm.mol2
m1 see above
o1 see above
sm (single molecule, ok not that obvious) means (an)
intra-molecular charge constraint is/are applied; so an additional
RESP fitting stage is carried out.
See
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/figure/F1/
All that is in the tutorials .
http://q4md-forcefieldtools.org/Tutorial/
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
I copy/cut an email I sent to the q4md-fft mailing .
http://lists.q4md-forcefieldtools.org/wws/info/q4md-fft
----------------------
- When a single molecule is involved in charge derivation a single
directory is generated by R.E.D. The mol2 files the user needs are
located in this unique directory.
- When multiple/$n molecules (let's say $n = 10 molecules) are
involved in charge derivation 10 'Mol_m$n' directories are generated
for the 10 molecules taken individually and sequentially. Then, a last
directory 'Mol_MM' is generated for the 10 molecules involved together
in a single charge fitting step. In your case the mol2 files you look
for are located in this 'Mol_MM' directory (the files located in the
'Mol_$n' directories are only interesting for comparison).
You can find examples of listing of files in the R.E.D. Server tutorial .
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
See for instance:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
with the corresponding PDF file that lists the files generated:
http://q4md-forcefieldtools.org/Tutorial/P2N/All-frag-Pept/listing-6mol.pdf
see also:
http://q4md-forcefieldtools.org/Tutorial/P2N/All-frag-Nuc/listing-2mol.pdf
In the Mol_MM directory you can find the following mol2 files:
- when an INTRA-MCC (with the remove or 'R' flag) is used for a
molecule X a FG2 fragment for X is generated
- when there is an INTER-MCC between 2 molecules A & B a FG1
fragment is generated for both A & B; atoms involved in an INTRA-MCC
are also removed from the FG1 fragment.
- when there is a unique INTER-MCC between two molecules A & B, an
additional FG fragment for the molecule B is generated; (this is the
case of the N-terminal and C-terminal fragments of an amino-acid; see
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24)
- when there are two & only two INTER-MCC between two molecules A &
B a list of
additional CT, OX & OY (2 topologies A & B) fragments are generated
for molecule B; (This is the case of the nucleotide fragments; see
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#26).
----------------------
regards, Francois
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Received on Mon Sep 26 2011 - 03:30:03 PDT
