AMBER Archive (2004)

Subject: AMBER: RED

From: Xin Hu (hux_at_mail.rockefeller.edu)
Date: Tue Jun 01 2004 - 18:02:37 CDT

Hi Francois,
Thanks for your help. Both RED and XRED works well on my workstation
(PC-linux).
One question, while I donot want to optimize the structure (for example, the
experimental structure), however, I had to generate the output .log file.
Can I simply change the RUNTYPE=ENERGY (for GAMESS) and run the RED.pl? I
try that but it did not work.

Another question regarding the parallel mode. I read the mannual and still
feel unclear. Do you mean using RED-SMP.pl instead of RED.pl to execute the
parallel computation? Since the optimzation on the basis set 6-31G* had to
be run in parallel (otherwise it is too time-consumming), I think it is good
to explain more about the parallel RED.

Hopefully to see your version 2.0 soon.

Thanks,

Xin 

---

----- Original Message ----- 
From: "FyD" <fyd_at_u-picardie.fr>
To: "Xin Hu" <hux_at_mail.rockefeller.edu>
Sent: Tuesday, June 01, 2004 2:08 PM
Subject: Re: question

> Hi,
>
> > I am very interested in RED. It is a powerful tool. One question is I
> > feel it is unconvenient to define the atom name in PDB files. Actually I
> > always get confused when I try to modify the atom name mannually.
> > Uauslly I get the PDB file (or Mol2 file) from Sybyl . Is there any
> > convenient way to convert the pdb or mol2 file to the right format to
> > input for RED?
>
> I know such part might not be seen as very convenient, but it is really
improved
> in the R.E.D. version 2.0 were the PDB names allows to generate also
> non-standard RESP inputs, using or not the "T" character...
> However, I think that the fact that the user has to 'think' about the RESP
> inputs is not that a bad think, after all... The proof: See below because
I
> think you did mistakes to prepare the PDB atom names for RESP input
> generation...
>
> For the automatic convertion of PDB/mol2 files, you can use babel.
> babel -ipdb toto.pdb -omol2 toto.mol2
> or
> babel -imol2 toto.mol2 -opdb toto.pdb
>
> But you still have to modify the PDB atom names manually...
>
> I do not really agree with the way you equivalenced your benzyl.pdb file:
I
> would use instead:
> ATOM      1  CT1 BEN     1       2.506   0.000   0.000
> ATOM      2  H1  BEN     1       2.872   0.268  -1.002
> ATOM      3  H1  BEN     1       2.872   0.733   0.733
> ATOM      4  H1  BEN     1       2.872  -1.002   0.268
> ATOM      5  C2  BEN     1       0.981   0.000   0.000
> ATOM      6  C3  BEN     1       0.281  -1.211   0.000 ortho
> ATOM      7  H3  BEN     1       0.824  -2.150   0.000
> ATOM      8  C4  BEN     1      -1.117  -1.211   0.000 meta
> ATOM      9  H4  BEN     1      -1.659  -2.150   0.000
> ATOM     10  C5  BEN     1      -1.816   0.000   0.000 para
> ATOM     11  H5  BEN     1      -2.900   0.000   0.000
> ATOM     12  C4  BEN     1      -1.117   1.211   0.000 meta
> ATOM     13  H4  BEN     1      -1.659   2.150   0.000
> ATOM     14  C3  BEN     1       0.281   1.211   0.000 ortho
> ATOM     15  H3  BEN     1       0.824   2.150   0.000
>
> The 'ortho' atoms to Methyl group should be equivalenced in the 1st RESP
input.
> Same for the 'meta'...
>
> > Attached is a very simple compounds benzyl group. I defined the methyl
> > carbone as CT1 (the three H1 H1 H1) and the six aromatic carbone as C2
> > C3 C4 C5 C6 C7 and the six equentlent hydrogen as H8. However, the
> > program doesn't work on it. No coordinations were wrote into the gamess
> > input file .inp.
> > Can you have a try?
>
> See http://www.u-picardie.fr/labo/lbpd/RED/bugs
> -------------  2nd bug report  ---------------------
>
> This bug has been corrected in the R.E.D. version 2.0
>
> > Another question, I try to use XRED.pl.  Both RED.pl and XRED.pl in the
> > working directory, but when I "start" the XRED, it shows no RED was
> > found. How to fix the problem?
>
> What is your O.S., machine, and 'wish' version?
> To use X RED you need 'wish version 8.3.5' (or newer) and to set XRED =
"on" in
> RED.pl line 1234; see RED.pdf manual page 5 and 8.
>
> > Thank you for your help.
>
> You are wellcome.
> Please ask your future questions in the AMBER mailing list.
>
> Kind regards, Francois
>
> F.-Y. Dupradeau
>  --
> The Scripps Research Institute, San Diego, CA
> Faculte de Pharmacie, UPJV, Amiens, France
>  --
> http://www.u-picardie.fr/labo/lbpd/fyd.htm
>

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