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?
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?
Beat Regards,
Tales
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Received on Tue Nov 08 2011 - 19:30:03 PST
