Reza,
maybe you want to have a look at the PyRED server
(
https://upjv.q4md-forcefieldtools.org/REDServer-Development/), which is
capable of doing RESP fits for AMBER in a reproducible way and also
provides documentation there.
On the AMBER website, there are several very helpful tutorials
(
http://ambermd.org/tutorials/) dealing with parameter derivation ("2
Developing Nonstandard Parameters").
If you still face problems then and are looking for help, you need to be
more specific in your question: What ist your intention, what exactly
did you do, what were the files you used, what are the errors.
Good luck.
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Univesität Erlangen-Nürnberg (FAU)
Germany
On 11/17/2021 01:03 AM, Reza Esmaeeli wrote:
> Dear Amber users,
>
> I’m trying to parametrize an artificial nucleotide while keeping the charge on certain atoms and the total charge fixed. I have already tried some suggestions from the mailing list, amber manual and the Advanced tutorial A1 to use QM calculations + resp but I’ve not been able to do it yet. I was wondering if you know of any straight-forward way of doing this before going deep into troubleshooting what I’m doing. I think I might be missing some examples or proper use of commands.
>
> Regards,
> Reza
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Received on Wed Nov 17 2021 - 01:00:02 PST
