[AMBER] Problem when visualizing bonds in VMD

From: Xiaoliu Zhang <xzhan91.lsu.edu>
Date: Wed, 17 Aug 2016 19:40:22 +0000

Dear Amber users,

I'm using amber with Amoeba force field following the Amber 16 manual, chapter 17.

After I got prmtop and inpcrd file by using tinker_to_amber command, I tried VMD to visualize my molecule. My Ambertool is 16 version and VMD is 1.9.1.

First i got an error:

AMBER 7 parm read error at flag section TITILE.

expected format %FORMAT(20a4) but got %FORMAT(a)

Then, I checked my topology file and found that it begins with this:

%VERSION VERSION_STAMP = V0001.000 DATE = 08/17/16 08:18:25
7box_5 ameoba FF

I changed the %FORMAT(a) to %FORMAT(20a4) by hand and ran again.

This time there's no error in terminal. However, no matter I choose VDW or CPK, there are only atoms showing on the screen, not any bond information at all.

Do you know how to fix this problem?

Thanks in advance.


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Received on Wed Aug 17 2016 - 13:00:03 PDT
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