[gmx-users] topology with all hydrogens

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Feb 6 11:58:24 CET 2011

Hi Mohsen,

Now I wouldn't want to get in the way of excellent ideas :)
Check the PRODRG FAQ. It is explained there (somewhere) how to force
inclusion of hydrogens.



On Feb 6, 2011 11:39 AM, "mohsen ramezanpour" <ramezanpour.mohsen at gmail.com>

Dear Dr.Tsjerk

I know it.I know PRODRG is not very valid for evaluating free
energies(According to Dr.Justin article) too.
But the problem is here:
If I know all of hydrigenes are polar,how can I have a topology with all of
Actually there are so many polar H in my small molecules which are not
included in topology file!!
These can change the number of Hydrogen bonds and as a resut my binding free

I want to do a new work about these,I have something excellent in my mind.
I only need a topology file with all hydrogenes in 43A1 force field.
Is there any way(except manually adding hydrogenes)?
Please let me know.
I will present  a new and excellent method instead of using PRODRG
Thanks in advance

On Sun, Feb 6, 2011 at 1:23 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> > Hi Mohsen, > > So ...

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