On Wed, Aug 17, 2016 at 3:40 PM, Xiaoliu Zhang <xzhan91.lsu.edu> wrote:
> 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?
>
You can't use AMOEBA topology files with VMD easily.
Try using a PDB as the topology instead.
HTH,
Jason
--
Jason M. Swails
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Received on Wed Aug 17 2016 - 13:30:02 PDT
