Dear Zhou Gong,
> 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?
You could use R.E.D. or Antechamber to execute RESP, or run RESP manually.
I suggest you to use R.E.D. or R.E.D. Server...
You can use a LEaP script or Antechamber to set the atom types of a
molecule (or you can do it manually in the LEaP program as well).
> 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
Once a FF library is generated using R.E.D. or Antechamber (mol2, prep
or off file formats), this FF lib. is loaded in LEaP and is generally
used to match the experimental structure available in a PDB file (here
the match appends only if the atom and residue names are identical in
the FF lib. and PDB file; if atoms such as hydrogen atoms are missing
in the PDB file, they are automatically added by LEaP in agreement
with these available in the FF lib).
You can find tutorials for such a task . q4md-forcefieldtools.org if
you do want to use R.E.D. or R.E.D. Server:
http://q4md-forcefieldtools.org/Tutorial/
Starting point:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
regards, Francois
> -----????-----
> ???: case [mailto:case.biomaps.rutgers.edu]
> ????: 2012?5?6? 9:42
> ???: AMBER Mailing List
> ??: Re: [AMBER] ??: 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 Sun May 06 2012 - 02:00:03 PDT
