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
%FLAG TITLE
%FORMAT(a)
7box_5 ameoba FF
%FLAG POINTERS
%FORMAT(10I8)
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.
Xiaoliu
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Received on Wed Aug 17 2016 - 13:00:03 PDT
