Re: AMBER: How can I read parm99.dat file?

From: Vineet Pande <>
Date: Thu, 05 May 2005 09:12:09 +0000

I would add to this thread asking a similar question, just to confirm
whether I understand the parm99.dat file correctly....also I ask a question
about Hydrogen of type HO parameters >>

In the first set of paramters:
CB 12.01 0.360 sp2 aromatic C, 5&6 membered ring
First Number is Mass and second number is radii?

Next, BOND, ANGLE, TORSION, and IMPROPER are fairly easy to understand...

In the next set of paramters following IMPROPER:
HO 0.0000 0.0000 OPLS Jorgensen, JACS,110,(1988),1657

For example whats the first and second term represent...first is
mass?....second in vdW something about well depth etc. ? but I am not clear
on this.....

Next, why do we not have any vdW parameters for HO....In the older force
fields we did have a paramter for this kind of hydrogen. I am expressing
this concern because in explicit solvent simulations I performed with a
kinase, hydrogen bonds in buried part of protein matrix turned out to be
very strong, more than usual and I attribute this to having no vdW
parameters for HO, which brings the two heavy atoms where HO is attached to
a donor, very close....this leads to a very strong electrostatic interaction
energy term, but at times an artifactual positive vdW interaction energy
term!.......Is there any justification for this?


>From: Bill Ross <>
>Subject: Re: AMBER: How can I read parm99.dat file?
>Date: Wed, 4 May 2005 17:12:08 -0700 (PDT)
>For an unbonded ion, only mass and vdw params need to be defined.
>Apparently both are done for I, and the mass line includes a
>value for polarizability. The main issue with the parameters
>is whether the vdw part is right. Given that there are bond and
>angle parameters, the vdw was presumably set for a covalently
>bonded I rather than I-, so this value would need to be
>overridden with a frcmod entry.
>It may not make much difference whether you use Cl- or I- if
>the ions are in water.
>Some discussion of radii (see 'IONIC RADIUS'):
>And a graph of ionic radii:
>The AMBER Mail Reflector
>To post, send mail to
>To unsubscribe, send "unsubscribe amber" to

Express yourself instantly with MSN Messenger! Download today it's FREE!

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu May 05 2005 - 10:53:00 PDT
Custom Search