AMBER Archive (2009)

Subject: Re: [AMBER] A problem with xleap and pdb file

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Feb 27 2009 - 07:56:26 CST

On Fri, Feb 27, 2009, nancy4619 wrote:

> Dear all , I have a problem when I load pdb file with order nan=loadpdb nanotube.pdb. My pdb file is about carbon nanotubes ,They are nanotube.pdb and nanotube.txt.The problem is in the Screenshot
> -1.png ,I don't know what is wrong with my pdb file and how to modify it,can any boby help me?
> Looking forwarding to your reply soon! Thanks a lot! Enjoy a good weekend!
> Nancy
>
>

> REMARK Nanotube Modeler PDB file (JCrystalSoft)
> REMARK Created:2009-2-18 17:10:05
> CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P1
> ATOM 1 C C A 1 3.887 0.000 0.000 1.00 0.00
> ATOM 2 C C A 1 3.697 1.201 2.115 1.00 0.00
> ATOM 3 C C A 1 3.887 0.000 1.410 1.00 0.00
> ATOM 4 C C A 1 3.697 1.201 3.525 1.00 0.00

All atoms in a given residue must have unique names. So, you would need
to name the atoms something like C1, C2, ....

Note that you will also need to create a leap unit for this structure.
You might Google for "nanotubes Amber" to see some previous discussion
about this topic. (Or, do the same search from the Amber web site, to
search the mailing list archives.)

...dac

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