Re: [AMBER-Developers] [AMBER] Alkali and Halide Monovalent Ion : paper

From: David A Case <>
Date: Tue, 6 Mar 2012 12:42:15 -0500

On Tue, Mar 06, 2012, CHAMI F. wrote:
> none of these frcmod is automatically loaded in tleap ...the default
> values are the one in parm99.dat (I copied them here)
> IM 2.47 0.1 Cl- Smith & Dang, JCP 1994,100:5,3757
> Li 1.1370 0.0183 Li+ Aqvist JPC 1990,94,8021. (adapted)
> IP 1.8680 0.00277 Na+ Aqvist JPC 1990,94,8021. (adapted)
> Na 1.8680 0.00277 Na+ Aqvist JPC 1990,94,8021. (adapted)
> K 2.6580 0.000328 K+ Aqvist JPC 1990,94,8021. (adapted)
> Rb 2.9560 0.00017 Rb+ Aqvist JPC 1990,94,8021. (adapted)
> Cs 3.3950 0.0000806 Cs+ Aqvist JPC 1990,94,8021. (adapted)
> MG 0.7926 0.8947 Mg2+ Aqvist JPC 1990,94,8021.(adapted)
> C0 1.7131 0.459789 Ca2+ Aqvist JPC 1990,94,8021.(adapted)

Note that these are only the "defaults" if you are loading a very old ions
lib, such as ions91.lib or ions94.lib. If you load ions08.lib, one should get
errors if the appropriate frcmod.ionsjc_xxx file is not loaded.

I'm cc-ing to Amber developers, since there are still a lot of leaprc files
(beyond those in the oldff directory) that load ions94.lib:

godel% grep ions9 *
leaprc.GLYCAM_06:loadOff ions94.lib
leaprc.GLYCAM_06EP:loadOff ions94.lib
leaprc.ff02pol.r1:loadOff ions94.lib
leaprc.ff02polEP.r1:loadOff ions94.lib
leaprc.ff03.r1:loadOff ions94.lib
leaprc.ff03ua:loadOff ions94.lib
leaprc.ff99SB:loadOff ions94.lib
leaprc.ff99SBildn:loadOff ions94.lib
leaprc.ff99SBnmr:loadOff ions94.lib
leaprc.ff99bsc0:loadOff ions94.lib
leaprc.ffAM1:loadOff ions94.lib
leaprc.ffPM3:loadOff ions94.lib
leaprc.pol12:loadOff ions94.lib

Some of these predate the JoungCheatham ("jc") work, and hence are probably
correct for historical reasons. But it seems odd that the GLYCAM and pol12
files are using ions94, could think about making changes for others in the
list above. So, comments from Tom, Carlos, Yong and the Glycam folks are
hereby solicited.


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Received on Tue Mar 06 2012 - 10:00:02 PST
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