Dear David
I followed your suggestion and use the xleap to deal with the PDB file.
However, another problems are occurred:
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
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
How do I deal with this?
Thanks for your kindness help
Best Regards!
Your sincerely:
Zhou Gong
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Biomolecular Physics and Modeling Group
Department of Physics
Huazhong University of Science and Technology Wuhan 430074, Hubei China
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-----ÓʼþÔ¼þ-----
·¢¼þÈË: David A Case [mailto:case.biomaps.rutgers.edu]
·¢ËÍʱ¼ä: 2012Äê5ÔÂ5ÈÕ 2:40
ÊÕ¼þÈË: AMBER Mailing List
Ö÷Ìâ: Re: [AMBER] add H-atoms automatic in tleap
On Fri, May 04, 2012, Zhou Gong wrote:
>
> I would like to perform the MD simulation of ubiquitin dimer (PDB ID:
> 1AAR). In this dimer molecule, the K48 in one molecule form the
> peptide linkage with the C-terminal of the other one.
Simplest(!?!) approach: load in the dimer pdb file in xleap, use the "edit"
command to get a visual window. Use the "erase" button to remove any extra
hydrogens (and the OXT atom in the C-terminal residue, if it is there), use
the "draw" command to add a bond between the N of K48 and the C-terminus,
then save the prmtop in the usual fashion.
....good luck...dac
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Received on Sat May 05 2012 - 08:00:02 PDT
