[gmx-users] errors with charmm36 ?

Justin Lemkul jalemkul at vt.edu
Tue Jan 14 17:44:19 CET 2014

On 1/14/14, 11:38 AM, Albert wrote:
> It is good to know that the c36 and CGenFF is actively update. I just noticed
> that this new version c36 no longer contains classic TII3P water models:
>   1: TIP3P   TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H
>   2: TIP4P   TIP 4-point
>   3: TIP5P   TIP 5-point
>   4: SPC     simple point charge
>   5: SPC/E   extended simple point charge
>   6: None
> So in priciple, we have to use CHARMM TIP3P model, is it correct?

You can use TIP3P without LJ terms on H atoms by making use of a "define" 
statement in the .mdp file; see ffnonbonded.itp for details.  We promote the use 
of the TIP3P model with LJ on H because it makes a huge difference for some 
systems, especially lipids.  Proteins are less sensitive to differences between 
the two TIP3P variants.  But strictly speaking, with CHARMM, we always use the 
TIP3P model with LJ terms on H atoms since that's what we do during parametrization.

> I am always wondering, would it be better if there is a tool that could convert
> the output from paramchem websever into a "single" ligand.itp file? The parachem
> website can export the results including all known information from CGenFF
> related to target ligand. In such compelte output file, it contains all
> necessary information for a ligand parameters and toplogy....

We're working on that.  Seamless integration between the different software 
packages is a goal we have.  For now, you'll have to hack the output a bit to 
make it syntactically correct.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list