From chemistry-request -8 at 8- server.ccl.net Thu Oct 19 16:22:09 2000 Received: from dagger.nd.edu (dagger.nd.edu [129.74.250.101]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA05368 for ; Thu, 19 Oct 2000 16:22:09 -0400 Received: from nd.edu (ruthenium.helios.nd.edu [129.74.220.44]) by dagger.nd.edu (8.10.2/8.10.2) with ESMTP id e9JKM8113781 for ; Thu, 19 Oct 2000 15:22:08 -0500 (EST) Sender: ptran _-at-_)nd.edu Message-ID: <39EF57F1.673117E8: at :nd.edu> Date: Thu, 19 Oct 2000 15:22:09 -0500 From: Pierre Tran X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry-: at :-ccl.net Subject: format problem Content-Type: multipart/alternative; boundary="------------11D753D5C6D6CFF85D2807BF" --------------11D753D5C6D6CFF85D2807BF Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, Is there a way to "map the atoms" of a pdb file of a crystal structure taken from Brookhaven data bank and use it in InsightII and perform minimization on it. The program complained and did not recognise the structure, here is the error message, when I tried to attribute the potentials : error: CRO:U8:C5' has open or undefined valences error: CRO:U8:C4' has open or undefined valences error: CRO:U8:C3' has open or undefined valences error: CRO:U8:O3' has open or undefined valences error: CRO:U8:C2' has open or undefined valences error: CRO:U8:C1' has open or undefined valences error: CRO:U8:N4 has open or undefined valences I need a program which allows the protonation of the structure and make it recognised by insightII and use it to perform minimization. Thank you. -- Pierre TRAN --------------11D753D5C6D6CFF85D2807BF Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all,

Is there a way to "map the atoms" of a pdb file of a crystal structure taken from Brookhaven data bank and use it in InsightII and perform minimization on it.
The program complained and did not recognise the structure, here is the error message, when I tried to attribute the potentials  :

error: CRO:U8:C5' has open or undefined valences
error: CRO:U8:C4' has open or undefined valences
error: CRO:U8:C3' has open or undefined valences
error: CRO:U8:O3' has open or undefined valences
error: CRO:U8:C2' has open or undefined valences
error: CRO:U8:C1' has open or undefined valences
error: CRO:U8:N4 has open or undefined valences

I need a program which allows the protonation of the structure and make it recognised by insightII and use it to perform minimization.
 

Thank you.
 
 

-- 
Pierre TRAN
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