Dear Francois,
Oh, really sorry for this carelessness. And thanks a lot.
Could I ask one more thing? I saw all the example files with around 25
atoms, is it the maximum number of atoms I should limit for each submitted
input file?
Thank you and sorry for inconvenience caused.
Chinhsu
On Tue, Oct 12, 2010 at 2:37 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Chinh Su,
>
> ok I got it; I used your name in the R.E.D. Server DB to get your
> account...
>
> R.E.D. IV generates the following error:
> Geometry optimization(s) is/are being computed for molecule 1 ...
> [ FAILED ] See the file(s) "JOB1-gau_m1-1.out"
>
> You have 2490 atoms with three zinc atoms...
>
> In the input submission page, it is written:
>
> "R.E.D. Server has been developed to compute RESP or ESP charge values
> embedded in force field library(ies) for small molecules and/or
> molecular fragments. It is not designed to handle large molecular
> systems such as a protein or an oligonucleotide.
> R.E.D. Server input files have to be carefully prepared. Do not
> hesitate to contact the q4md-forcefieldtools team if you have
> questions about these inputs using the Assistance service or the q4md
> force field tools mailing list."
>
> If you want to get a FF library with RESP charges for a bio-inorganic
> complex, you need to isolate the amino-acids which participate in the
> 'active site'.
> You need to know which theory level you will use in QM and you need to
> know how to build a molecular fragment in order to incorporate your
> active site in your protein... See
> http://q4md-forcefieldtools.org/Tutorial/
>
> Do not hesitate to ask if you have more specific questions...
>
> regards, Francois
>
>
> > I uploaded my p2n file to the RED server to calculate atomic charges for
> my
> > molecule, but keep getting errors from the result as below:
> >
> > *"Error termination via Lnk1e in /usr/local/g03-userred/l103.exe at Mon
> Oct
> > 11 10:40:27 2010.
> > Job cpu time: 0 days 0 hours 0 minutes 6.6 seconds."
> > *
> > I was using Mode 1 in the RED with Gaussian to either optimize geometry
> and
> > compute the charges.
> >
> > Meanwhile, I used the perl package for RED-vIII.4. pl too, but got the
> > error in insufficient memory for Gaussian (g09) running.
> >
> > Please help. I have tried 4 times, but still got stuck.
> >
> > Thank you.
> >
> > chinsu
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 12 2010 - 00:30:03 PDT
