Hello!
The Amber14 manual has some very helpful instructions for tinker_to_amber
(pages 275-277).
Which FF are you using? Did analout run just fine? Are you keeping the file
naming consistent?
I just did a test using Tinker7.1 with the tinker_to_amber included in
Amber18 using the dhfr test case included in Tinker7 and
the amoebabio09.prm file included with Tinker7. Using the most current
amoebabio09.prm (included with the latest release) did not work with
Tinker7.
$ $tinker7/analyze dhfr PC > dhfr.analout
$ $tinker7/xyzpdb dhfr.xyz
$ $AMBERHOME/bin/tinker_to_amber -name dhfr -title "DHFR AmoebaBio09 FF"
The one thing I noticed is that the .prm file can't have the .prm extension
when using tinker_to_amber, as it gets appended as part of the code (so
amoebabio09.prm.prm). It's also crucial that all 3 box lengths are defined
in the key file (even if it's cubic and 1 would do for Tinker).
Key files are a little different between Tinker7 and Tinker8 (because of
the addition of anglep, if I understand correctly). This means that an
xyz/key pair in Tinker7 might not work in Tinker8, and one that works for
Tinker8 might not work for Tinker7. Most of the differences between the
src/etc/tinker_to_amber.F90 shipped with AmberTools14 and AmberTools18 deal
with indentation.
Sincerely,
Emmett Leddin
Pronouns: he/him
Chemistry PhD Candidate
On Thu, Nov 19, 2020 at 3:47 PM Michael Sonny Miller <millerms.stanford.edu>
wrote:
> Hi,
>
> I'm having trouble getting any version of tinker_to_amber to work.
> I have tried using the Amber18 and the Amber14 versions with Tinker 8 and
> Tinker 7.1 respectively, and get errors about not finding information in
> the analout file.
> Is there a guide somewhere or examples of exactly what release of Tinker
> is required for each Amber release, and how exactly one is supposed to use
> tinker_to_amber?
>
> Thank you in advance.
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Received on Wed Nov 25 2020 - 13:00:02 PST
