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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 22 2011 - 00:30:03 PDT
