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
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Received on Thu Nov 24 2022 - 10:30:03 PST
