Dear Francesco,
Sorry I missed your email; when you have questions related to R.E.D.
Server better send your queries .
http://lists.q4md-forcefieldtools.org/wws/info/q4md-fft ; there, the
number of emails is far smaller/should not be missed and mainly
related to q4md-fft, charge derivation and FF development.
> I have to simulate a protein made by three iron sulphur cluster, namely
> one 4Fe4S, one "canonical" 3Fe4S and one "not-canonical" 3Fe4S.
> The topic of the research is the caracterization of the overall protein
> structure, so I don't need an accurate representation of the clusters.
> Although I found CHARMM parameters for the 4Fe4S and 3Fe3S clusters, I
> prefer using AMBER-ILDN force-field. Comparisons with other force-fields
> show that AMBER-ILDN is the best parameter set to describe protein features.
Yes, mixing two FF is always a bad idea (there is a web page in the
Gromacs web site related to this problem). That being said you could
test if these CHARMM parameters do lead to good results when
associated with AMBER-ILDN.
> So regarding my protein, I guess I can use AMBER for protein. For the
> iron-sulphur clusters it is enough constraining
> bonds,angles and dihedrasl among the S and Fe atoms. The problem are
> atomic charges.
>
> I've been running GAMESS-US, both as stand-alone and RED-server, but it
> fails to converge both with or without geometry optimization.
When? at the first optimization step?
> I am using the BLYP/6-31+G* model.
Several comments/questions/suggestions here:
R.E.D. Server provides GAMESS, Firefly and Gaussian 2003 and 2009.
- did you try all these programs?
- did you try R.E.D. Server 'Development'?
- you can run R.E.D. Server and R.E.D. IV in two modes
http://q4md-forcefieldtools.org/REDS/popup/popredmodes.php
this means you can provide a QM geometry optimization output (obtained
on your workstation) to R.E.D. IV (MEP computation is always carried
out with NoSymmetry)
- if you provide us the R.E.D. Server code (PXXX) of your calculations
that failed we can look at your data and try to help.
- we also have hidden submission procedures with many new features
related to transition metal complexes (with a totally new R.E.D. IV
code). If we think this is needed we can provide these links.
- finally we can create user defined options within new
specific/submission procedures; just tell us your needs in this case.
> I've three main questions to address:
> 1) Has anyone some input file suitable for the RESP-charges calculation
> with GAMESS-US?
Sure - R.E.D. interfaces Gaussian/GAMESS/firefly. Charges are highly
reproducible independently of the QM program interfaced (see
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/ for a discussion)
We do use these three QC codes . q4md-forcefieldtools.org; each code
has its own advantages. Concerning transition metal complexes, all our
new developments are carried out with the Gaussian 09 program so far.
We plan to try to extend this new features when using GAMESS and
Firefly. Did you try using Gaussian 2009?
> 2) Is there any simple rule, or a software, that can help me to
> calculate iron multiplicity for iron containing molecules?
For instance using
http://www.webelements.com/ Ex: Iron
- click on Fe
->
http://www.webelements.com/iron/
- click on Electron shell properties
->
http://www.webelements.com/iron/atoms.html
Ground state electron configuration: [Ar].3d6.4s2 of Iron
Fe3+ for instance is consequently [Ar].3d5: 5 electrons in 5 d orbitales
- if 5 single electrons: spin multiplicity = 6 (i.e. I I I I I)
- if 3 single electrons: spin multiplicity = 4 (i.e. II I I I °)
- if 1 single electron: spin multiplicity = 2 (i.e. II II I ° °)
Spin multiplicity is the number of single electron(s) + 1
See also
http://en.wikipedia.org/wiki/Spin_multiplicity
- With a single metal atom this is quite simple.
- With several metal atoms the difficulty is when you want to set
different spin multiplicities for different metal centers...
> 3) Are parameters for the 3Fe4S avalaible for the AMBER force-field?
I do not know.
> Any advice doesn't contained in the above questions is well apreciated.
I am not sure you have used all the options of R.E.D. Server ;-)
regards, Francois
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Received on Tue Nov 01 2011 - 01:30:03 PDT
