Subject: adding protons

From: Vlad Cojocaru <[email-masked]>
Date: Mon, 26 Aug 2002 19:25:08 +0200

Dear CCL-ers,
   This email would be better sent to AMBER list but it seems that the 
AMBER list is out of order these days.
    I have a pdb file with a piece of RNA. I will run dynamics with it. 
The problem is that the pdb does not have protons. I tried to use 
protonate for the purpose but it does not work at all for nucleic acids. 
On the other hand Leap is adding by default the protons. So, the 
question is: Is the default add by Leap reliable or should I use o more 
reliable way. If the latter can somebody suggest a freeware that can be 
used for this purpose?
    Maybe also a bit of discussion about the importance of initial 
positions of the protons for a MD run ....especially for Nucleic Acids.
   Thanks a lot in advance for any kind of Replies.
   Best regards,
vlad

-- 
Vlad Cojocaru 
Max Planck Institut for Biophysical Chemistry 
Deparment: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1389 
e-mail: [email-masked]

---

From: Daquan Gao <[email-masked]>
Date: Mon, 26 Aug 2002 14:53:45 -0500

In my opinion, the initial hydrogen positions are not very important,
except that it might flip the chirality if the hydrogen is on a chiral
center and the initial position is "too bad".

I don't have any freeware for this, macromodel does a good job if the
correct connectivity is given (meaning the bonds between the heavy atoms
are correct), but not free. I think reinventing the wheel by writing a
small script is not that hard. Basically you look for the plane of the
three atoms if the hydrogen is connected to a carbon in between two other
heavy atoms, and then form a perpendicular plane. Then put hydrogens in
the plane. Checking number of hydrogens that are already there and
connectivity is probably somewhat tedious. 

regards, 
daquan

On Mon, 26 Aug 2002, Vlad Cojocaru wrote:

> -= This is automatically added to each message by mailing script =-
> [email-masked] -- To Everybody  | [email-masked] -- To Admins
> Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: [email-masked]
> 
> 
> 
> 
>