AMBER Archive (2009)

Subject: Re: [AMBER] ATP/GTP parameters

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Tue Sep 01 2009 - 01:10:41 CDT

Dear Eduardo,

> Hello Francois, can you send those parameters to me as well?.
> It would be nice if you post the link for all to see ^_^

Which ones ? If you really need all of them, we can submit them in
R.E.DD.B. right away. All is ready, we just have to submit...

> I was wondering if you can send me all those nice parameters you have
> for phosphates...

All ? No until they are registered in R.E.DD.B. // a R.E.DD.B. code
has been generated. However, if you provide me the list of the
cofactors you need for your calculations, we can try to provide these
co-factors to your personal email.

> also, could you give me some feedback as to what
> software to use to visualize the MEP?
> The swiss-pdb viewer for example calculates the MEP but this is based
> on the atomic charges, and I would like to use the mesh
> generated by gamess-UK/gaussian to visualize the MEP....

For the web, we use Jmol http://jmol.sourceforge.net/.
See the projects in R.E.DD.B.; For instance:
http://q4md-forcefieldtools.org/REDDB/projects/W-46/JavaApplet-1.php
http://q4md-forcefieldtools.org/REDDB/projects/W-46/JavaApplet-2.php
   up to
http://q4md-forcefieldtools.org/REDDB/projects/W-46/JavaApplet-10.php

To create images, we use molekel:
http://q4md-forcefieldtools.org/RED/images/RED.jpg

Then,
VMD, GaussView, Gabedit etc...

Finally, when you submit emails in the q4md-fft mailing list (@
q4md-fft_at_q4md-forcefieldtools.org) you need to be registered.
Consequently, your last email was not submitted in the q4md-fft
mailing list.

regards, Francois

> FyD wrote:
>> Dear Steve,
>>
>>> I am looking for GTP parameters and looked in the achieves. I
>>> found that ATP and GTP had been deposited on the AMBER homepage
>>> site. However, looking through all the links, I cannot find them.
>>> Have they been incorporated into the newer force
>>> field/parameters? (I have AMBER 8 addition.)
>>
>> If you are interested I can send you ATP, GTP force field libraries
>> or any co-factors you might be interested in deriving from XYP (X
>> = A, C, T, G, dA, dC, dT, dG. Y = M D T Q etc... An even more...).
>>
>> This force field topology database has been developed in a single
>> R.E.D. job. Many co-factor analogs can be constructed since a
>> building block approach has been followed. See the list of
>> cafactors built:
>> http://archive.ambermd.org/200812/0329.html
>>
>> regards, Francois

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