AMBER Archive (2005)

Subject: RE: AMBER: How to make PDB file by myself

From: Vineet Pande (pande_vineet_at_hotmail.com)
Date: Tue Jan 25 2005 - 05:06:42 CST

Did u try insight...

>From: "Mayumi Haga" <haga_at_cir.tohoku.ac.jp>
>Reply-To: amber_at_scripps.edu
>To: <amber_at_scripps.edu>
>Subject: AMBER: How to make PDB file by myself
>Date: Tue, 25 Jan 2005 13:23:32 +0900
>
>Dear Sirs.
>
>I am using amber7and 8,
>I want to ask you about how to make PDB format file of HOPG(graphite)
>substrate. It consists only of carbon, so the amount of C atoms has got
>huge.
>
>I made PDB format file by using Gauss View, there are about 8000atoms. I
>tried to read this PDB format file by XLEaP, successed to read atoms with
>many errors, but these atoms were not connected.
>
>I tried to make PDB format file by Chem3D, though it contains binding
>infomation, XLEaP could only read untill 1000 carbon atoms.
>
>I couldn't find how to read large amount of C atoms by XLEaP. untill 1000
>atoms, it could read by using C1-C999 as a atom name. and atom type CT .
>But
>I couldn't read over 1000 atoms. Should I change residue number or residue
>name?
>
>I want to know how to make PDB format files like artificial substrate by
>myself.
>
>Sincerely yours
>
>Mayumi
>
>******************************************************************
>Mayumi Haga
>
>Kawano Laboratory, Center for Interdiscipinary Research,
>Tohoku University, Japan
>*******************************************************************
>
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