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