Dear Evgenii,
Thank you for using py_resp.py and pointing out these issues. For your
specific task, if you are only interested in the traditional point-charge
model, my current recommendation for you is still using the resp program,
which is still available in AmberTools.
Regarding the incompatibility issue of py_resp.py with antechamber, we are
actively working with its developer Prof. Junmei Wang to allow antechamber
to recognize the -t charge file of py_resp.py. For respgen, we are
developing a new respgen program for generating input files for py_resp.py
with the flexibility of choosing point-charge, induced-dipole or
perm-dipole models. The updated antechamber program and respgen program
will be available in AmberTools2023.
Best,
Shiji Zhao
On Thu, Nov 24, 2022 at 10:06 AM Евгений Кадцын via AMBER <amber.ambermd.org>
wrote:
>
> Dear experts,
>
> I have recently tried to use AmberTools2022 for non-standard residues
> parametrization as described in some classical tutorials. There is a stage
> of charge calculation using the RESP procedure. As I understand, a new
> utility py_resp.py is suggested to use for this purpose instead of old
> resp . But the output format of the new program differs from the old one,
> especially the format of the charge file (-t key). The old files contain
> the charges only in an order, in which atoms are arranged in a molecular
> input file, and there is much more information in the new file format. And
> the worst thing is that antechamber which should use these files to assign
> charges to atoms cannot understand them now, an error «Unable to find
> charges in file (filename). Verify the filename and the file contents»
> arises.
> I have tried the command:
> antechamber -i ace_leuol.mol2 -fi mol2 -o ace_leuol_aharged.ca -o ac -c
> rc -fc ace_leuol.qout2
> and charge file ace_leuol.qout was obtained by:
> py_resp.py -i ace_leuol.respin1 -o ace_leuol.respout1 -t ace_leuol.qout1
> -e ace_leuol.esp
> py_resp.py -i ace_leuol.respin2 -o ace_leuol.respout2 -q ace_leuol.qout1
> -t ace_leuol.qout2 -e ace_leuol.esp -ace_leoul.newesp
> I’ve attached qout2 and mol2 files.
> As I understand, the only choice now is to rewrite charges from qout to ac
> file manually. Am I right or there is some way to do it using antechamber ?
> If it is the only way, then I just inform you about the problem (have not
> seen in FAQ) and hope that it will be fixed soon :)
> Another similar problem is related to the incompatibility of new
> py_resp.py and old respgen. py_resp.py has the default options ipol=5 and
> ipermdip=1 , and respgen creates respin files with these default values,
> while no atomic dipole values are used. Maybe there is some way to fix it
> except the manual addition of these keywords to the respin files or it also
> is worth to fix this behavior?
>
>
>
> With best regards,
> Evgenii Kadtsyn_______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
>
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Received on Mon Nov 28 2022 - 21:00:02 PST
