Hi all,
I'm following the procedure reported in a previous message to connect
the ends of a peptide.
In my case
~ribbon
display
delete :41@oxt
bond :1@n: 41@c
After, I run minimization, but I have the following message
Charge model: AMBER ff14SB
Total charge for #0: 0.810
The following residues had non-integral charges:
SER 1.A 0.8102
1 model(s) had non-integral total charge
Details in reply log
Residue #0:1.A (SER/serine) is missing atom H_1
In my model SER1 has two hydrogens named H2 and H3. Now the nitrogen has
four covalent bonds that is unusual.
If, before connecting residues 1 and 41, I add hydrogens to the molecule
I obtain SER1 with 3 hydrogens. After I remove H2 and H3 and repeat the
procedure, in the minimization step I obtain the message that H3 is
missing...
Any suggestion?
Thanks
Marco
--
Marco Sette, PhD
Associate Professor of Molecular Biology
Department of Chemical Sciences and Technology
The University of Rome, "Tor Vergata"
Via della Ricerca Scientifica, 00133, Rome, Italy
e-mail:sette@uniroma2.it
Tel.: +39-0672594424
Fax: +39-0672594328
