Thank you very much. :)
2011/11/9 Jason Swails <jason.swails.gmail.com>
> On Tue, Nov 8, 2011 at 10:06 PM, Tales Yuan <yukitenkou.gmail.com> wrote:
>
> > Dear Amber Users,
> >
> > I want to use LEaP to prepare a pdb file, but I have two questions.
> >
> > 1. The protein has to CYS with disulfide bridge. I have changed CYS to
> CYX
> > in pdb file, and added the "bond" command in leap.in file like this:
> >
> > .
> > .
> > .
> > bond protein.45.SG protein.67.SG
> > .
> > .
> > .
> > savepdb protein leap_model_wat.pdb
> >
> > When I check the new pdb file "leap_model_wat.pdb", the S-S bond can't be
> > displayed with Chimera. I opened the file, there was no CONNECT
> information
> > at the end. I use "ambpdb" or "ptraj" to convert the .rst/.traj file to
> > .pdb, there was also no CONNECT information. The atom connect information
> > maybe stored in the .prmtop file. So if I want to see the S-S bond in
> > Chimera or some other tools, should I add the CONNECT information at the
> > end of pdb file manually?
> >
>
> Leap doesn't print CONECT records, as far as I know (PDB printing I think
> was more of an afterthought, really, since LEaP was really meant to write
> OFF libraries and topology files). If the topology file has the bond,
> that's all that's necessary.
>
> If you need the CONECT records, you'll need to add them yourself (note, I
> think it's CONECT, not CONNECT, but I would look at the PDB standard to be
> sure).
>
>
> > 2. I prepared the protein file using SYBYL. If the hydrogens could be
> > recognized correctly by LEaP, should I delete H atom and add them in
> LEaP?
> > Or maybe I could keep them?
> >
>
> I'm not sure what you're asking here (did you forget a "not" somewhere?)
> If LEaP complains about unknown hydrogen atoms, then the naming is wrong
> and you have 2 options. 1) Rename all of the hydrogens to the "proper"
> name stored in the library files. 2) Delete those hydrogens and just let
> LEaP add them.
>
> If LEaP doesn't complain, and it saves a topology file, there's nothing
> wrong with using those hydrogens.
>
> HTH,
> Jason
>
>
> > Beat Regards,
> >
> > Tales
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Wed Nov 09 2011 - 06:00:03 PST
