Dear Jason,
>> Some time ago there were 'some' discussions about this tutorial: I
>> have no problem writing - rewriting - repeating -
>> whatever_is_the_world_used_here that I do not agree with the charge
>> derivation procedure, which is presented in this tutorial: I do not
>> think this approach should be followed by a new user.
>
> ?At the end of the day, it's a multi-conformational RESP fit using a
> HF/6-31G*-derived MEP, which fits the prescription for the Merz-Kollman
> charge derivation scheme. It also shows users how resp works, which they
> can then take and extend to include multiple orientations, for instance.
In a tutorial one can indeed present multiple conformation charge fit
in a wrong way. One can present wrong options in charge derivation in
the name of... One can pretend mastering charge derivation. etc...
This is exactly what I think is done in this tutorial.
> There is value to providing a workflow that can be scripted and run on a
> computer in which all components of the workflow can be downloaded and
> installed locally. The perl RED scripts are candidates, but you regularly
> discourage their use in favor of a solution that is only available through
> a web interface.
Yes - I discourage by now the use of R.E.D. perl (& its server
version) because PyRED is far more simple to use (this P2N file format
is finally in the bin! chemical equivalencing is robust even in crazy
cases, etc... obviously there is still a learning curve) and PyRED
presents many new features (atom typing, frcmod generation, energy
decomposition, extra-point models, polarizable charge model by now,
user defined options, etc...).
Yes - So far, PyRED is only available through R.E.D. Server Dev... We
do what we can ;-) this will change in the future for sure. But PyRED
is obviously based on R.E.D. perl, which is based on the work of
Cieplak et al. The followed charge derivation philosophy is here the
same.
Yes - This tutorial does not present RESP charge derivation as I think
it should do done for Amber: i.e. where was originally developed the
RESP charge model.
- the 2 stage procedure is skipped: this is bad for a _RESP_
tutorial I mean in a pedagogic purpose i.e. for new users: atomic
charges are just numbers.
- the use of the RESP program is not classical & even border line;
this has to be discouraged considering how RESP was designed (i. e.
not that user friendly)
- has the qin file to be manually prepared? Is it tractable in a
multiple mep approach? Is it a joke?
- the use of intra-molecular charge constraint is simply
'inadequate' here. One defines such constraints for individual atoms,
which are kept in the molecular fragment not for a capping group (see
the common N, H, C, O charge values of the backbone of the hydrophobic
amino-acids in the Cornell et al. FF).
- some affirmations are simply wrong - point!
- some keywords are 'curiously' justified: is it science or what? :-P
- what about conformations in a multiple mep approach? :-P I guess...
- etc, etc...
At the end of the day ;-) I might upset some people with this email.
Sorry for that. I'll have to live with that. This is just my personal
opinion.
regards, Francois
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Received on Thu Apr 02 2015 - 01:00:02 PDT
