[gmx-users] topology with all hydrogens
tsjerkw at gmail.com
Sun Feb 6 11:58:24 CET 2011
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>
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 ...
gmx-users mailing list gmx-users at gromacs.org
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users