[gmx-users] topology with all hydrogens

[mohsen ramezanpour]

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
them?
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
energy!!!


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
Mohsen

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

> Hi Mohsen,
>
> So you want to have a topology with all atoms for use in a united atom
> force field? Seems a bit awkward... PRODRG will only include polar
> hydrogens, in accordance with the GROMOS force field. It won't be a
> particular trustworthy topology, though, but you've probably caught the
> words of caution expressed regularly on this list.
>
> Cheers,
>
> Tsjerk
>
> On Feb 6, 2011 9:42 AM, "mohsen ramezanpour" <ramezanpour.mohsen at gmail.com>
> wrote:
>
> Dear All
>
> I want to generate a topology file in 43A1 force field for a small
> molecule.
> Of course I want one which contains all hydrogens in that.
> PRODRG doesn't generate like this.do you know another server with these
> conditions?
>
> Thanks in advance
> Mohsen
>
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