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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Nov 08 2011 - 20:30:03 PST
