Re: [AMBER] bond connections

From: mohammad r <>
Date: Sun, 6 Dec 2015 08:59:33 +0000 (UTC)

Thank you Jonathan,
In vmd when I load both the top and crd files with Amber 7 restart, it shows nothing. Indeed when loading the topology file the number of atoms and frames are zero but when I load the crd file the number of atoms and frames changed. 

    On Sunday, December 6, 2015 12:11 PM, Jonathan Sheehan <> wrote:

> On Sat, Dec 5, 2015 at 1:19 AM, mohammad r <> wrote:
>> Thank you Jason,
>> Unfortunately I cannot open the image you've sent to me(I tried paint and
>> windows photo viewer). Can you please send it in another format?

Dear Mohammad,

Here's a fixed image of the molecule.  You can see many severe
distortions. You need to go back and correct those, as Jason said.

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Received on Sun Dec 06 2015 - 01:00:06 PST
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