Re: Different solvents

From: Marc Baaden (
Date: Sun Nov 13 2005 - 07:49:19 CST

Dear Gaurav,

I am currently trying to adapt some parameters for chloroform models
for use with NAMD. There are a number of issues that I would like to
point out first, but the parameter files and some sample run inputs
are available on my website [1]. As this is work in progress, please
use these files with care and report back any errors.

As I am still quite a novice concerning NAMD, some of the issues might
just be related to my ignorance. The only chloroform model (by Chang,
Dang and Peterson) that I have so far implemented is a fully rigid one,
and it is not obvious to me how to implement this in NAMD. I previously
used this with hacked version of Amber, where you specified bonds and
angles between all 5 atoms and could then fix those.
With NAMD I could not find a way to do this (without hacking the code). It seems
only bonds including hydrogen can be fixed, and angles cannot be constrained.
So for now I use high force constants.
Furthermore I get an error when defining Cl-H "bonds" unless I use rigidAtoms
none and splitPatch position which is less efficient than rigidAtoms All
(which only works if I deactivate the Cl-H "bonds").

So one question would be how can/should fully rigid molecules be implemented
for use with NAMD ?

By checking the forcefield parameters, I also checked the ones used for
TIP3P water (which I will use together with the chloroform) and it seems
to me as if the parameters that come with NAMD do not correspond to the
original paper [2]. For instance there are non bonded parameters for the
hydrogen in eg par_all22_prot.inp whereas Jorgensen only put a non bonded
term on the oxygen. So the water parameter file at [1] corresponds to the
original parameters from [2].

Does anybody know where the discrepancy in par_all22_prot.inp come from ?
(Maybe this is more a CHARMM than a NAMD issue ?)

If other people have parameterised chloroform models for NAMD I would be
very interested to hear about this.

Marc Baaden

[2] Jorgensen et al., JCP, 79 (1983) 926

>>> Gaurav Sharma said:
>> Hi All,
>> I would like to simulate a protein in solvents other than water such
>> chloroform, acetone, dimethylmethylphosphonate (DMMP) etc.
>> Are there parameters available for such solvents. Someone on the list
>> suggested using VEGA ZZ to generate the solvent which is fine, but we
>> still need the parameter file to run the simulations.
>> Many thanks,
>> Gaurav

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris      -
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

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