Hello Paul,
The CPIN format has been modified in Amber18, and the file you sent is in the new format. Therefore, I believe you have not used AmberTools16 to generate this file. The new file format is not compatible with Amber16. However, there is an option in cpinutils.py that allows you to generate the CPIN file in the Amber16 format. Type “cpinutils.py —help” to check this out.
Unfortunately, cysteine pKa predictions are bad with our CpHMD method, and this should be the case for igb=8 as well. We know the reasons why this happens and what are the modifications necessary in Amber to fix that, however, these have not been released yet.
Best,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633<tel:+1(352)846-1633>
On Jul 2, 2020, at 9:29 AM, Paul Meister <meisterp.uwindsor.ca> wrote:
[External Email]
Hello,
I'm trying to run constant pH REMD on a protein system following this
tutorial: https://urldefense.proofpoint.com/v2/url?u=http-3A__jswails.wikidot.com_ph-2Dremd&d=DwIBaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vg8iTdivJL1PEwCvcH8P2DFF-Rtc9lAQvIqnaSWm1Pc&m=NySSg8-LIRzPvoJg08ehwXn0bqH5W5tEhXWGGRnHZZI&s=FXEny1I0aQzTwdO6eKCMUAs-qtkGkgk9H92dYACS49U&e= . Everything worked up until
the point where I started running the equilibration step. After submission,
I get the following error message:
At line 174 of file constantph.F90 (unit = 18, file = 'sufs.cpin')
Fortran runtime error: Bad data for namelist object statene
Does anyone know why this error pops up? I tried searching this error in
the archive but didn't find a solution.
I generated the cpin file as directed in the tutorial and have attached it
to this message. I'm mostly interested in finding the pKa of the residues
His123, Lys226, and Cys367. For reference, I'm using Amber16 and the
version of cpinutil.py is 16.0. I also used igb=8 instead of igb=2 as
recommended for catalytic cysteine residues in some recent publications.
Thank you,
Paul
--
Paul Meister
B. Sc. Honours Biochemistry
Ph.D. Candidate in Biochemistry
Computational Enzymology Research Assistant
<sufs.cpin>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vg8iTdivJL1PEwCvcH8P2DFF-Rtc9lAQvIqnaSWm1Pc&m=NySSg8-LIRzPvoJg08ehwXn0bqH5W5tEhXWGGRnHZZI&s=UOf8vc6WQeHAkJwyubGLhDQytmpr0DEmJkO9wrVpjXI&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 03 2020 - 08:30:04 PDT
