R.E.D. II FAQ

R.E.D. II Frequently Asked Questions

Below, you will find a summary of FAQ gleaned from the net. Most of them come from the AMBER (and GAMESS) mailing lists. Questions are written in green color and the corresponding answers in black...

Please check also the AMBER mailing list archives (http://structbio.vanderbilt.edu/archives/amber-archive/ and http://amber.ch.ic.ac.uk/archive/) and AMBER Web site (http://amber.scripps.edu/Questions/resp.html and http://amber.scripps.edu/Questions/amber-archive.html) for other information about R.E.D. and X R.E.D.

1) Announcement of the release of program R.E.D. version 2.0
2) How to use geometry optimization ouput file(s) from NWChem, Q-CHEM, or Jaguar in R.E.D.-I or R.E.D.-II ?
3) How to use R.E.D. output(s) in AMBER or other programs ?

1) Announcement of the release of the R.E.D. program, version 2.0

From: FyD <fyd@u-picardie.fr>
Date: July, 1st, 2005

Dear Amber users,

I am pleased to announce the release of the R.E.D. program, version 2.0., http://www.u-picardie.fr/labo/lbpd/RED/.

We developed the R.E.D. I program (RESP ESP charge Derive, version 1.0) to automatically derive 'RESP' and 'ESP' charges starting from an un-optimized PDB structure. R.E.D. sequentially executes (i) either the "GAMESS" program or the "Gaussian" program to optimize the target structure and to compute the corresponding MEP, and (ii) the "RESP" program to fit the atom-centered charges to the grid previously determined. Format conversions needed during the procedure and "GAMESS", "Gaussian" and "RESP" inputs are automatically generated by R.E.D. By controlling the molecular orientation of the optimized geometry, a new RESP fitting procedure based on multi-orientation feature is proposed and allows getting highly reproducible 'RESP' and 'ESP' charges whatever the QM software and starting Cartesian coordinates are.

With R.E.D. II (version 2.0), multi-conformation RESP and ESP fit has been implemented, and can also be automatically carried out using a well defined set of molecular conformations. Thus, 'multi-conformation' and 'multi-orientation' RESP fit can be performed together or independently according to the user choice. 'Standard' but also 'non-standard' RESP inputs can now be generated. The geometry optimization ouput generated by one of the two QM programs can be used as input for MEP computation using the second QM program. Finally, RESP and ESP charges can be derived for chemical elements having up to a total number of electrons, Z = 35. And much more...

Thus, R.E.D. makes the derivation of the 'RESP' and 'ESP' charges a straightforward, simple and highly reliable procedure.

R.E.D. has been written with the "Perl" programming language, and X R.E.D. with the "tcl/tk" programming language, making these two programs highly flexible and portable. R.E.D. and X R.E.D. have been tested on PC-LINUX and SGI-IRIX workstations, but should work on all other UNIX platforms. They are "free" (i. e. provided at no cost) for academic users after signing a license. On the contrary, a fee is demanded to commercial users for the use of R.E.D. & X R.E.D.

- A new manual has been written taking into account most of the problems discussed in the AMBER mailing list.
See http://www.u-picardie.fr/labo/lbpd/RED/RED-II.pdf

- The FAQ about R.E.D. I has been updated, and contains now more than 50 FAQs.
See http://www.u-picardie.fr/labo/lbpd/RED/FAQ-I.htm
- The FAQ about R.E.D II will be updated and is be available at:
http://www.u-picardie.fr/labo/lbpd/RED/FAQ-II.htm

- The six bugs reported for R.E.D. I, http://www.u-picardie.fr/labo/lbpd/RED/bugs-I, have been corrected.
- The future bugfixes for the R.E.D. II bugs will be available at http://www.u-picardie.fr/labo/lbpd/RED/bugs-II

- The X R.E.D. graphical interface, http://www.u-picardie.fr/labo/lbpd/RED/XRED.htm, has been updated to execute R.E.D. II.

- Finally, all the users which used a R.E.D.-II beta version, should re-download R.E.D.-II since new features have just been added in the final version.

Best 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

2) How to use geometry optimization ouput file(s) from NWChem, Q-CHEM, or Jaguar in R.E.D.-I or R.E.D.-II ?

From: FyD <fyd@u-picardie.fr>
Date: Sat, 04 Jun 2005

I have a QM geometry optimization output which was obtained using Q-CHEM. Is there a way to use this file in Molecular Electrostatic Potential (MEP) computation and charge derivation using R.E.D. ?

Yes, you have to modify the format of the optimized Cartesian coordinates originating from Q-CHEM (or whatever the QM software is)... In fact, you have to convert this set of optimized Cartesian coordinates to the GAMESS-US or Gaussian format.

- For GAMESS:
First, provide the GAMESS-US author names as it is printed in a regular GAMESS ouput:
******************************************************
* GAMESS VERSION = 22 NOV 2004 (R1) *
* FROM IOWA STATE UNIVERSITY *
* M.W.SCHMIDT, K.K.BALDRIDGE, J.A.BOATZ, S.T.ELBERT, *
* M.S.GORDON, J.H.JENSEN, S.KOSEKI, N.MATSUNAGA, *
* K.A.NGUYEN, S.J.SU, T.L.WINDUS, *
* TOGETHER WITH M.DUPUIS, J.A.MONTGOMERY *
* J.COMPUT.CHEM. 14, 1347-1363(1993) *
*************** SILICON GRAPHICS VERSION *************

Then, add the "GAMESS-US set of words" describing that the target minimum has been found "EQUILIBRIUM GEOMETRY LOCATED" followed by the Q-CHEM optimized Cartesian coordiantes to the GAMESS-US format:
EQUILIBRIUM GEOMETRY LOCATED Manually added !
COORDINATES OF ALL ATOMS ARE (ANGS)
ATOM CHARGE X Y Z
------------------------------------------------------------
H 1.0 -1.0926929407 1.0006752165 -0.0006637553
C 6.0 -0.7175066981 -0.0131933065 0.0000739164
H 1.0 -1.0984884477 -0.5206794658 -0.8830165874
H 1.0 -1.0982148650 -0.5192957108 0.8840754754
[Cut...]

Finally, add the words describing that the GAMESS job has finished normally...
EXECUTION OF GAMESS TERMINATED NORMALLY

- For Gaussian:
Apply a similar strategy: First, provide the Gaussian author names as it is printed in a regular Gaussian ouput:
M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria,
M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, Jr.,
R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam,
A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi,
V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo,
S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui,
K. Morokuma, N. Rega, P. Salvador, J. J. Dannenberg, D. K. Malick,
A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski,
J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko,
P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox,
T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe,
P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, J. L. Andres,
C. Gonzalez, M. Head-Gordon, E. S. Replogle, and J. A. Pople,
Gaussian, Inc., Pittsburgh PA, 2002.

Then, add the "Gaussian set of words" describing that the target minimum has been found "Stationary point found" followed by the Q-CHEM optimized Cartesian coordiantes to the Gaussian format (as a Gaussian "Standard orientation"):
Stationary point found Manually added !

Standard orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 1 0 1.076629 0.975959 -0.000004
2 6 0 0.655547 -0.019723 0.000000
3 1 0 1.012855 -0.543371 0.883550
4 1 0 1.012856 -0.543378 -0.883545
[Cut...]
---------------------------------------------------------------------

Finally, add the words describing that the Gaussian job has finished normally...
Normal termination of Gaussian

Thus, R.E.D. will consider this file as a GAMESS-US or Gaussian geometry optimization output which has successfully finished. You will be able to load this file (let's name it "QM-out.log") as a R.E.D. input using the following R.E.D. variables $OPT_Calc = "Off", $MEPCHR_Calc = "On", $JOB_OPT = "./QM-out.log".
The choice of converting such Q-CHEM, NWChem or Jaguar (whatever the QM software is) geometry optimization output into GAMESS or Gaussian format does not really matter if R.E.D.-II is used since R.E.D.-II can load GAMESS QM output for MEP computation using Gaussian (and vis-versa).

3) How to use R.E.D. output(s) in AMBER or other programs ?

From: FyD <fyd@u-picardie.fr>
Date: Sat, 25 Jun 2005

I'm working through the RED tutorials in the version 1 manual. I think I understand modifying the RED.pl file. I'm not sure HOW the data is output (what format) and where to find it (this isn't mentioned in the manual). I'm using g03 on a sunray system. Also, how do you use the output info from RED with antechamber?

The final R.E.D. format is a Tripos mol2 file (See http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0). You have to load this mol2 file in LEaP to be able to generate a LEaP OFF library and/or the corresponding prmtop/prmcrd files... Below, are two examples of AMBER8/LEaP scripts allowing to convert a Tripos mol2 file into a LEaP OFF library:

- Converting a whole type molecule such as a small solvent molecule or a ligand:
# "Mol_o.mol2" is the Tripos file to be converted
MOL = loadmol2 Mol_o.mol2
# Define the force field (FF) atom types of each atom (if needed)
# 'atom_name$n' & 'atom_type$n' being the 'atom name' & 'FF atom type' of the atom_number $n
set MOL.1.atom_name1 type atom_type1
...
set MOL.1.atom_name$n type atom_type$n
# Save the OFF library
saveoff MOL MOL.off

- Converting a molecule fragment compatible with pre-existing fragments:
# The Tripos fragment is going to be a 'central' new amino-acid
MOL = loadmol2 Mol_o.mol2
# Set the _molecule_ properties
set MOL name "MOL"
set MOL head MOL.1.N
set MOL tail MOL.1.C
# Set the _residue_ properties
set MOL.1 connect0 MOL.1.N
set MOL.1 connect1 MOL.1.C
set MOL.1 restype protein
set MOL.1 name "MOL"
# Save the OFF library
saveoff MOL MOL.off

Many programs can recognize the Tripos format and can use it directly. Indeed, this file format is very convenient since many information can be available in this file (atomic charges, atom name and residue name, atom connectivities and force field atom types). For using the Tripos format in CHARMM, this file format might have to be converted into .psf file using some scripts...

To be continued...

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