pdb-l: q4md-forcefieldtools.org announcement

FyD fyd at q4md-forcefieldtools.org
Fri Nov 25 05:37:06 PST 2011


Dear All,


I am pleased to announce the official release of the latest  
developments at http://q4md-forcefieldtools.org.

q4md-forcefieldtools.org regroups an ensemble of tools, server,  
database and tutorials related to empirical force field developments.  
Theses developments are designed for the AMBER and GLYCAM force  
fields, but can also have applications in CHARMM and OPLS force field  
based simulations.

At the basis of our work is the RESP and ESP charge Derive (R.E.D.)  
program devoted to RESP and ESP charge derivation and force field  
library building for new molecules and potentially any type of  
molecular fragments. The approach leads to reproducible charge values  
independently of the quantum chemistry program interfaced or initial  
structure chosen by the user. In complex approaches, multiple  
molecules, multiple conformations and multiple orientations are  
involved in charge derivation and force field library building, and a  
large set of force field libraries or Force Field Topology DataBase  
(FFTopDB) is generated. The procedure is now compatible with any type  
of biomolecules and bioinorganic molecules (nucleic acids, proteins,  
glycoconjugates, organic and bioinorganic structures in the ground or  
excited states; covalently or non-covalently bound; natural structures  
as well as chemically engineered or artificial analogs).

. The standalone version of the R.E.D. tools is available at  
http://q4md-forcefieldtools.org/RED/.
. R.E.D. Server available at http://q4md-forcefieldtools.org/REDS/ is  
a Web server, which provides all required software and hardware for  
charge derivation and force field library building. It interfaces the  
latest versions of the Ante_R.E.D. and R.E.D. programs.
. R.E.DD.B. is a database of RESP and ESP charges and force field  
libraries available at http://q4md-forcefieldtools.org/REDDB/.
. Related tutorials are at http://q4md-forcefieldtools.org/Tutorial/.


* New web tools have been developed in R.E.D. Server allowing the  
automatic and simultaneous generation of force field libraries for the  
nucleotide or amino-acid fragments.
. N-terminal, C-terminal and central fragments for a new amino-acid  
residue from a single dipeptide
      http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
. 5'-terminal, 3'-terminal and central fragments for a new nucleotide  
residue from a single nucleoside
      http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#27

* A new R.E.D. Server version named "R.E.D. Server Development" has  
been developed.
R.E.D. Server Development allows RESP and ESP charge derivation and  
force field library building for new molecules and fragments involving  
all the elements of the periodic table. Several user defined options  
have been also incorporated in this server.
  See http://q4md-forcefieldtools.org/REDS-Development/
      http://q4md-forcefieldtools.org/REDS-Development/faq.php
      http://q4md-forcefieldtools.org/REDS-Development/faq.php#17

* New R.E.DD.B. features have been developed representing the first  
step toward R.E.DD.B. 2.0, a database of Force Field Topology DataBase.
  New scripts have been written allowing the automatic submission in  
R.E.DD.B. of data generated by the R.E.D. tools and R.E.D. Server.
  See http://q4md-forcefieldtools.org/REDDB/faq.php#5
  PubMed ID indexation is now incorporated in R.E.DD.B.
  New Force Field Topology DataBases are available. Among others see  
representative examples:
      http://q4md-forcefieldtools.org/REDDB/projects/F-88/
      http://q4md-forcefieldtools.org/REDDB/projects/F-87/
      http://q4md-forcefieldtools.org/REDDB/projects/F-85/

* A new force field library file format has been developed within the  
LEaP program (AmberTools 1.5).
  The mol3 force field library file format was developed. This file  
format merge some advantages of the Tripos mol2 and AMBER OFF file  
formats within t/xLEaP.
  See http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php

* Updated RESP version 2.2 for charge fitting for metal complexes and  
large set of molecules, conformations and orientations.
  See http://q4md-forcefieldtools.org/RED/resp/

* Tutorials have been updated accordingly to these new features.

* The articles describing R.E.DD.B., R.E.D. and R.E.D. Server are all  
freely available under the following PubMed Central reference number:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238896/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125739/


All our tools and data are open to all, and are in agreement with the  
GNU General Public License 3.0.

regards, Francois

           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/



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