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
>> regards, Francois
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Received on Tue Jun 04 2013 - 05:30:02 PDT
