Dear David
Thanks for your help. But I still have some questions
The way you said such as redistribute the residual charge, or use RESP,
and change the atoms types of N atoms. Are these operation can be done in
the Xleap?
If I couldn't done these in Xleap, next time, when I load the pdb file
into the leap, it will add the extra H-atoms again.
Could you please tell me how to deal with these by hand
Thank you!
Best Regards!
Your sincerely:
Zhou Gong
-----ÓʼþÔ¼þ-----
·¢¼þÈË: case [mailto:case.biomaps.rutgers.edu]
·¢ËÍʱ¼ä: 2012Äê5ÔÂ6ÈÕ 9:42
ÊÕ¼þÈË: AMBER Mailing List
Ö÷Ìâ: Re: [AMBER] ´ð¸´: add H-atoms automatic in tleap
On Sat, May 05, 2012, Zhou Gong wrote:
>
> 1. after I delete the H atoms and draw the bond between N of K48
> and C-terminus, the xleap show the charge for the total system is not
> integer and cannot save prmtop files
It is true that you have to adjust the charges around the connection, so
that now you have a neutral lysine and a neutral c-terminal residue. You
could define a molecule that is (or resembles) the linkage you want, and use
RESP (e.g. through the R.E.D. web site) to get charges. Or you could make
the new peptide bond have the same charges as all other peptide bonds, and,
if there is just a small residual charge to redistribute, do that by hand.
>
> 2. after I draw a bond between N of K48 and C-terminus, the new
> parameters for the new bonds are lacked in force field, the xleap show
> " no torsion terms for O-C-N3-CT, CX-C-N3-CT etc
The lysine N atom is no longer an N3, but an N; similar changes in atoms
types may be needed for other atoms in the vicinity of the new linkage.
Basically, you want to make the new peptide linkage look as much as possible
like other peptide groups in your protein.
...good luck....dac
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Received on Sat May 05 2012 - 19:30:02 PDT
