Dear Anselm,
Thank you for your reply. I already solved the naming problem. I got new
warnings. Please find attached the input and output files for tleap.
It seems like the "bond" commands I used doesn't work. Just let you know,
the protein I am working with is a glycoprotein, so I used "bond" command
to make the glycan and protein interaction.
As you can see in the output file, I got warnings about improper torsions.
How to solve the problem? Thank you.
Best regards,
Rui
On Thu, Jul 4, 2019 at 5:43 AM Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> Hello Rui,
>
> to learn the atom names of the specific glycans, you may use xleap:
>
> After sourcing the glycam force field, use the edit command to visualize
> the 3D structure of the carbohydrate of interest in a separate window
> and then have its atom names depicted via "Display" -> "Names". This
> should enable you to find the corresponding atom names for manual
> substitution in your input pdb file.
>
> Regards,
>
> Anselm
>
>
> > I added glycans to a protein using CHARMM GUI, because when I used
> GLYCAM,
> > the glycans I added have severe steric clashes.
> >
> > However, CHARMM GUI and GLYCAM have different naming format. In order to
> > use LEaP to prepare the glycoprotein to do MD simulation, I almost
> manually
> > modified all the differences, except for the H2N, C2N, O2N and CME. I
> > could't find the meaning of these specific atom types. Because it seems
> > like LEaP doesn't understand the pdb file generated by CHARMM GUI.
> >
> > How can I solve the problem?
> >
> > Looking forward to your reply.
> >
> > Best regards,
> > Rui
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/octet-stream attachment: g1dr9.in
- application/octet-stream attachment: leap.log
Received on Thu Jul 04 2019 - 10:00:02 PDT
