Dear George,
> It sounds like it is a lot easier if I use the R.E.D server where the
> work-flow has been automated, right?
you first run R.E.D. Server/Ante_R.E.D. 2.0 & then re-run R.E.D.
Server/R.E.D. IV after having checked/modified (if needed) the p2n
file generated by Ante_R.E.D.
PDB --> P2N ---> mol2
please see: http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#1
We are aware these 2 steps are a limiting factor by now; the main
advantage is that the user can modify the P2N file(s) after its
generation and this makes the system quite flexible and allows
handling complex cases of charge derivation
With R.E.D. python all is combined in one step. But in this case the
code is far more 'sophisticated'.
> I saw that the server interfaces either with Ante_R.E.D. 2.0 or R.E.D. IV
> program. Can you tell me what is the difference and which one should I
> use?
Please read the tutorials; in short you first execute Ante_R.E.D. to
generate the P2N file(s) using PDB file(s) as input and then using the
P2N file(s) you execute RED in a second step
> Just to double check: is this approach suitable for a methyl-histidine
> residue that is a part of a protein (actin)? I will extract this residur
> from the original pdb file and then upload it to the server.
You extract this residue from the protein (or you construct it by
controlling the conformation i.e. the phi, psi and chi dihedrals),
transform it into a dipeptide (PDB file to be transformed into P2N
file) and then from this dipeptide you generate the central (and
N-term & C-term) fragments (to be re-inserted in your protein) using
R.E.D. Server/R.E.D.
See:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#16
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17
then all together:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
and finally all together automatically from a single dipeptide:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
regards, Francois
> Dear George,
>
>> Does R.E.D. III.x need a GAMESS installation which the perl script will
> somehow locate?
>
> See the installation procedure described in the RED version II pdf file.
> http://q4md-forcefieldtools.org/RED/RED-II.pdf
> See the part "-III- HOW TO USE R.E.D. & X R.E.D.?" page 9
>
> i.e. you need to:
> - Install GAMESS (or Firefly or Gaussian) _and_ RESP.
> - Check that GAMESS (Firefly or Gaussian) works from your X-terminal.
> (i.e. the binaries and scratch path are defined and found)
> - Same remark for RESP: install & test it before interfacing it with R.E.D.
> you can use the standalone version of the RESP program from our web site:
> http://q4md-forcefieldtools.org/RED/resp/
>
>>> From R.E.D. III.x, we obtain a Tripos mol2 file that we can directly
> then
>> load into leap and get the .lib and .frcmod files we want?
>> After loading the mol2 file into leap, do we need to run some kind of
> script to change atomnames etc?
>
> If you use R.E.D. Server/Ante_R.E.D. 2.0 atom names are checked (i.e. in
> the philosophy of a FF library two atoms can NOT share the same name in
> a given residue). See
> http://q4md-forcefieldtools.org/REDS/news.php#2
>
> Once you got the mol2 file(s) from R.E.D. perl you need to add the FF
> atom types; here we do use a LEaP script and define eaxh FF atom types
> using the 'set' command.
> See for instance:
> http://q4md-forcefieldtools.org/REDDB/Projects/W-46/
> http://q4md-forcefieldtools.org/REDDB/Projects/W-46/script1.ff
>
> regards, Francois
>
> PS With R.E.D. Python all is done automatically from a PDB file.
>
>
>>> Dear George,
>>>> I was wondering if any user has constructed a lib/prep and a frcmod
>> file
>>>> for a methylated histidine to share with me.
>>>> If no, what is the general procedure to make these files?
>>>>> From the tutorial:
>> http://ambermd.org/tutorials/advanced/tutorial1_adv/
>>>> I understand that a RESP calculation must be made with R.E.D to get
> the
>> partial charges.
>>>> Then, I think some AmberTools must be used but I am not sure which.
>>> See Figure 1 at
>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#0
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Received on Thu Jun 06 2013 - 00:30:02 PDT
