Dear Francois,
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...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). 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)
All the best,
Th.
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: Donnerstag, 22. September 2011 09:26
An: AMBER Mailing List
Betreff: Re: [AMBER] bug in respgen ?
Dear Thomas,
The derivation of RESP or ESP charges and the generation of force
field library(ies) for the different fragments of a modified
amino-acid are now automatically handled by R.E.D. Server. By
providing a single P2N file for the dipeptide (ACE-XXX-NME; XXX = your
asymmetric sulfoxyde cyo amino-acid) of a modified amino-acid a
researcher can use R.E.D. Server/R.E.D. IV to generate the force field
libraries and charge values for the Central, the N-terminal and
C-terminal fragments as well as for the dipeptide molecule in a single
approach/R.E.D. IV job.
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
versus
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
At the end the user get a set of mol2 files to be loaded in LEaP.
I would like to underline that R.E.D. Server version 2.0 is open to
all - even to private companies. Please see:
http://q4md-forcefieldtools.org/REDS/faq.php#2
http://q4md-forcefieldtools.org/REDS/faq.php#3
regards, Francois
Quoting thomas.fox.boehringer-ingelheim.com:
> Hi,
>
> Im using respgen (amber11 release) to generate resp input files, and
noticed
> that in my setting the generated resp input has an additional empty line
> between the atom/ivary block and the lagrange block, meaning that the
> lagrangians are not read in.
>
> Here the command
>
> respgen -i cyo.ac -o respin.1 - f resp1 -a residue.dat -n 1
>
> Can you reproduce the error? I have attached the inputfiles cyo.ac and
> residue.dat, for whoever wants to take a closer look. I have looked into
the
> code, from there I would assume that the fprint statement in line 337 is
too
> much, at least for my case, but I don't want to simply take it out in case
> other inputs need it...
>
> Thanks,
> Th.
>
> -----------------------cyo.ac--------------------------
> CHARGE 0.00 ( 0 )
> Formula: H12 C6 N2 O3 S1
> ATOM 1 C1 CYO 0 4.027 0.068 0.395 0.000000 c3
> ATOM 2 H11 CYO 0 4.048 1.017 0.918 0.000000 hc
> ATOM 3 H12 CYO 0 4.224 -0.723 1.111 0.000000 hc
> ATOM 4 H13 CYO 0 4.803 0.046 -0.356 0.000000 hc
> ATOM 5 C2 CYO 0 2.697 -0.198 -0.271 0.000000 c
> ATOM 6 O3 CYO 0 2.591 -0.891 -1.247 0.000000 o
> ATOM 7 N4 CYO 0 1.621 0.382 0.316 0.000000 n
> ATOM 8 H4 CYO 0 1.712 0.884 1.172 0.000000 hn
> ATOM 9 C5 CYO 0 0.279 0.138 -0.151 0.000000 c3
> ATOM 10 H5 CYO 0 0.327 0.027 -1.226 0.000000 h1
> ATOM 11 C6 CYO 0 -0.557 1.353 0.249 0.000000 c
> ATOM 12 O7 CYO 0 -0.503 1.771 1.375 0.000000 o
> ATOM 13 C8 CYO 0 -0.283 -1.146 0.480 0.000000 c3
> ATOM 14 H81 CYO 0 -0.412 -1.012 1.546 0.000000 h1
> ATOM 15 H82 CYO 0 0.399 -1.968 0.313 0.000000 h1
> ATOM 16 S9 CYO 0 -1.896 -1.657 -0.160 0.000000 s4
> ATOM 17 H9 CYO 0 -1.427 -1.834 -1.405 0.000000 hs
> ATOM 18 O10 CYO 0 -2.188 -2.988 0.423 0.000000 o
> ATOM 19 N11 CYO 0 -1.341 1.882 -0.703 0.000000 n
> ATOM 20 H2 CYO 0 -1.241 1.570 -1.640 0.000000 hn
> ATOM 21 C12 CYO 0 -2.175 3.040 -0.443 0.000000 c3
> ATOM 22 H121CYO 0 -1.584 3.945 -0.364 0.000000 h1
> ATOM 23 H122CYO 0 -2.881 3.146 -1.255 0.000000 h1
> ATOM 24 H123CYO 0 -2.716 2.899 0.480 0.000000 h1
> BOND 1 1 2 1 C1 H11
> BOND 2 1 3 1 C1 H12
> BOND 3 1 4 1 C1 H13
> BOND 4 1 5 1 C1 C2
> BOND 5 5 6 2 C2 O3
> BOND 6 5 7 1 C2 N4
> BOND 7 7 8 1 N4 H4
> BOND 8 7 9 1 N4 C5
> BOND 9 9 10 1 C5 H5
> BOND 10 9 11 1 C5 C6
> BOND 11 9 13 1 C5 C8
> BOND 12 11 12 2 C6 O7
> BOND 13 11 19 1 C6 N11
> BOND 14 13 14 1 C8 H81
> BOND 15 13 15 1 C8 H82
> BOND 16 13 16 1 C8 S9
> BOND 17 16 17 1 S9 H9
> BOND 18 16 18 2 S9 O10
> BOND 19 19 20 1 N11 H2
> BOND 20 19 21 1 N11 C12
> BOND 21 21 22 1 C12 H121
> BOND 22 21 23 1 C12 H122
> BOND 23 21 24 1 C12 H123
>
------------------------------------------------EOF--------------------------
> -----------
>
------------------------------residue.dat------------------------------------
> --
> //predefined charges in a format of (CHARGE partical_charge atom_ID
> atom_name)
> CHARGE -0.415700 7 N4
> CHARGE 0.271900 8 H4
> CHARGE 0.597300 11 C6
> CHARGE -0.567900 12 O7
> //charge groups in a format of (GROUP num_atom net_charge)
> GROUP 12 0.00000
> //atoms in the group in a format of (ATOM atom_ID atom_name)
> ATOM 7 N4
> ATOM 8 H4
> ATOM 9 C5
> ATOM 10 H5
> ATOM 11 C6
> ATOM 12 O7
> ATOM 13 C8
> ATOM 14 H81
> ATOM 15 H82
> ATOM 16 S9
> ATOM 17 H9
> ATOM 18 O10
>
-------------------------------------------EOF-------------------------------
>
> Mit freundlichen Grüßen / Kind regards,
> Dr. Thomas Fox
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Received on Fri Sep 23 2011 - 06:00:02 PDT
