**From:** Ben Roberts (*Ben.P.Roberts_at_vcp.monash.edu.au*)

**Date:** Mon Sep 27 2004 - 01:35:23 CDT

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Hi Matthew,

David has told me that you are most likely after how to convert parameters

from Gromacs to Charmm format.

Before I begin, I need to point out that I don't actually have all the

information you need. I have provided everything except for dihedrals.

This is because the Gromacs force field uses a different type of function

(for proper and improper dihedrals) than the Charmm force field. Gromacs

appears to use harmonic and periodic functions while Charmm uses modified

Fourier series.

My apologies for this, my work up to this point has been using the OPLS-AA

force field which is more similar to the Charmm force field, so I didn't

realise this difficulty!

There are four sorts of parameters, however, which can be easily

converted, and I've covered each of these in the rest of the email below.

I hope this helps.

Best regards,

Ben

ATOMIC PARAMETERS

Charge and Mass

Source: Gromacs topology (.top) file eg from PRODRG

Destination: Charmm topology (.psf) file

Conversion: None necessary, charges and mass use standard atomic units

BONDING PARAMETERS

Reference Distance and Force Constant

Source: Gromacs topology (.top) file eg from PRODRG, or, if it is not in

there, it will be in one of Gromacs' master 'included topology' (.itp)

files

Destination: Charmm parameter file (can be called anything, but most

commonly .inp or .prm)

Conversion

----------

Reference Distance: Multiply Gromacs by 10 to get Charmm (this is because

Gromacs works in nm and Charmm in angstroms)

Force Constant: Divide Gromacs by 824.8 to get Charmm (this is because of

a J to Cal conversion, the aforementioned factor of 10 squared, and a

factor of 2)

ANGLE PARAMETERS

Reference Angle and Force Constant

Source: Gromacs topology (.top) file, or, if not there, in the appropriate

Gromacs master 'included topology' (.itp) file

Destination: Charmm parameter file

Conversion

----------

Reference Angle: No conversion necessary

Force Constant: Divide Gromacs by 8.248 to get Charmm (J to Cal

conversion, and a factor of 2)

VAN DER WAALS PARAMETERS

Sigma and Epsilon

Source: Gromacs topology (.top) file, or if not there, the .itp file

Destination: Charmm parameter file

Conversion

----------

Sigma: Multiply Gromacs by 10, then multiply the result by half the 6th

root of 2 (net result is about 5.6123102)

Epsilon: Divide Gromacs by -4.184

The VDW section of NAMD actually has two sigma entries and two epsilon

entries for each atom. The second one is for 1,4-scaled interactions. The

relationship between them is:

Sigma (scaled) = Sigma (unscaled)

Epsilon (scaled) = 0.5 * Epsilon (unscaled)

I hope this information may be useful to people.

Best regards,

Ben

----------------------------------------------------------------------

Benjamin P. Roberts, B.Sc.(Hons)

Ph.D. Student

Department of Medicinal Chemistry

Victorian College of Pharmacy (Monash University)

381 Royal Parade, Parkville VIC 3052, Australia

Phone +61 3 9903 9674 | Fax +61 3 9903 9582 | Mobile +61 401 784 940

----------------------------------------------------------------------

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