RE: AMBER: How to make PDB file by myself

From: Vineet Pande <>
Date: Tue, 25 Jan 2005 11:06:42 +0000

Did u try insight...

>From: "Mayumi Haga" <>
>To: <>
>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
>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 .
>I couldn't read over 1000 atoms. Should I change residue number or residue
>I want to know how to make PDB format files like artificial substrate by
>Sincerely yours
>Mayumi Haga
>Kawano Laboratory, Center for Interdiscipinary Research,
>Tohoku University, Japan
>The AMBER Mail Reflector
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Received on Tue Jan 25 2005 - 11:53:01 PST
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