FyD Home Page

Publications

NMR & Mol. Modeling software

LINUX & UNIX

AmberFFC

FF Parameter Development

RESP ESP charge Derive

RESP ESP charge DDataBase

RESP ESP charge Derive Server

q4md-forcefieldtools.org



NMR & Molecular Modeling software links





Our 8 dual Athlon CLUSTER (under LINUX):

We compiled and use GAMESS, PC-GAMESS, Gaussian & AMBER on "nautilus"

http://nautilus.u-picardie.fr/ganglia/


Molecular modeling software, we use:

AMBER:

http://amber.scripps.edu/

http://amber.ch.ic.ac.uk/


InsightII and even more...:

http://www.accelrys.com/


VMD:

http://www.ks.uiuc.edu/Research/vmd/


WHATIF and the WHATIF Web Interface:

http://www.cmbi.kun.nl/whatif

http://www.cmbi.kun.nl:1100/WIWWWI/


Hyperchem:

http://www.hyper.com


GAMESS (US) and PC-GAMESS:

http://www.msg.ameslab.gov/GAMESS/GAMESS.html

http://classic.chem.msu.su/gran/gamess


Information about compiling GAMESS (US):

http://www.chm.tu-dresden.de/edv/gamess99/comp.html

http://www.sgi.com/industries/sciences/chembio/resources/gamess_us/

http://lacebark.ntu.edu.au/gamess/faq.html

http://nmr1.ioc.ac.ru/Staff/AnanikovVP/gamess/gamg77.htm


Gaussian:

http://www.gaussian.com


Rasmol:

http://www.umass.edu/microbio/rasmol


Babel:

http://smog.com/chem/babel/


Openbabel:

http://openbabel.sourceforge.net/



NMR software with a 500 MHz Bruker AVANCE, we use:

GIFA:

http://www.cbs.univ-montp1.fr/GIFA/welcome.html


XWIN-NMR:

http://www.bruker-biospin.com/nmr/products/software.html



Software databases:

http://cmm.info.nih.gov/modeling/software.html

http://zeus.polsl.gliwice.pl/~nikodem/linux4chemistry.html

http://www.arl.hpc.mil/PET/cta/ccm/archive/webs/ffield.html

http://www.ks.uiuc.edu/Development/biosoftdb/



Free literature searches:

Medline:

http://www4.infotrieve.com/newmedline/search.asp

Pubmed:

http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed


Article-INIST:

http://services.inist.fr/public/eng/conslt.htm




Useful databases:

Protein data bank:

http://www.rcsb.org/pdb/

http://pdbbeta.rcsb.org/pdb/Welcome.do


Cambridge Cristallographic Database:

http://www.ccdc.cam.ac.uk/


EMBL Nucleotide Sequence Database:

http://www.ebi.ac.uk/embl/


SWISS-PROT (protein sequence Database):

http://www.ebi.ac.uk/swissprot/



Other interesting stuffs, we use:

Sequence Retrieval System:

http://www.expasy.ch/srs5/


BLAST and FASTA:

http://www.ncbi.nlm.nih.gov/BLAST/

http://fasta.bioch.virginia.edu/

http://www.ebi.ac.uk/fasta33/


IUPAC nomenclature home page:

http://www.chem.qmw.ac.uk/iupac/

http://www.iupac.org/



Mailing lists, we use:

AMBER mailing list:
Subscribe => majordomo@scripps.edu
Queries => amber@scripps.edu
Archives => http://structbio.vanderbilt.edu/hypermail/amber-archive/date.phtml

GAMESS mailing list:
Queries => gamess@lists.ciw.edu
Archives => https://lists.ciw.edu/mailman/listinfo/gamess

VMD mailing list:
Queries => vmd-l@ks.uiuc.edu
Archives => http://www.ks.uiuc.edu/Research/vmd/mailing_list/

Jmol mailing list:
Queries => jmol-users@lists.sourceforge.net
Archives => http://lists.sourceforge.net/lists/listinfo/jmol-users

PDB mailing list:
Queries => pdb-l@sdsc.edu
Archives => https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l

CCL mailing list:
Subscribe => chemistry-request@ccl.net
Queries => chemistry@ccl.net
Archives => http://www.ccl.net/chemistry/resources/messages/index.shtml



Journals, publications & Magazines:

ACS publications:

http://pubs.acs.org/about.html


Wiley journals:

http://www3.interscience.wiley.com/journalfinder.html


Elsevier and Academic Press journals:

http://www.sciencedirect.com/science/journals


Springer international journals:

http://link.springer.de/ol/index.htm


An interesting journal list at the Cambridge University Chemical Laboratory:

http://www.ch.cam.ac.uk/ChemJournals.html



General software (i. e. word processing, plotting, curve fitting software), we use:

Abiword:

http://www.abisource.com/

Openoffice:

http://www.openoffice.org/


Grace:

http://plasma-gate.weizmann.ac.il/Grace/




Last update of this web page: March, 19th, 2007