Hello Amy,
Ok, I understand. Two questions:
1) How did you generate this cpin file? Did you modify the titratable_residues.py file inside parmed to do that? (This is what I would do)
2) Could you please send me off the list your input files so I can reproduce your issue?
Best,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Amy Rice <arice3.hawk.iit.edu>
Sent: Thursday, November 1, 2018 3:49:47 PM
To: AMBER Mailing List
Cc: Cruzeiro,Vinicius Wilian D
Subject: Re: [AMBER] CpH simulation- error reading charges in long cpin file
Thank you for the help! I first tried running finddgref.py with 3_site.cpin, and had the STATENE as 0.000000,DELTAGREF,DELTAGREF,DELTAGREF, as you mentioned. However, the problem is not with finddgref.py directly, but with the constant pH simulation step in amber. To simplify troubleshooting, then, I switched to running CpH simulation and set the reference energies all back to 0 as they are in the cpin files I provided.
The commas I mentioned are from the error that is output when I run with the 3 site cpin files-
"Cannot match namelist object name 0.090.09-0.180.090.09-0.180.090.09-0.180.09"
The object name it is trying to match (0.090.09-0.180.090.09-0.180.090.09-0.180.09) is a series of the charges from my cpin file, but the commas are missing. The commas are present in the cpin file, but for some reason they are not being recognized when the file is being read in. This only occurs with the 3 site cpin files (3_site.cpin and 3_site_copy.cpin), but not the 1 site or 2 site versions. I hope this clarifies the problem I am having!
On Thu, Nov 1, 2018 at 2:34 PM Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu<mailto:vwcruzeiro.ufl.edu>> wrote:
Hi all,
I was attempting to run finddgref.py to calculate the reference energy of a custom titratable residue. The python script failed with the following (unhelpful) error message:
------------------------------------------------------
ERROR: The execution of AMBER using the binary /share/apps/amber/18/bin/pmemd.cuda failed. The execution returned the following STDERR:
At line 167 of file constantph.F90 (unit = 23, file = 'test.cpin.temporary')
--------------------------------------------------
When I look at the mdout file, there is no additional information, it merely ends with:
--------------------------------------------------
Implicit solvent radii are ArgH and AspGluO modified Bondi2 radii (mbondi3)
|reading charge increments from file: test.cpin.temporary
-----------------------------------------------------
Next, I tried setting all the reference energies to 0 in the cpin file and running CpH directly. The simulation again fails at the step where the cpin file is read in. This time I get a slightly more helpful error message:
----------------------------------------------------
At line 167 of file constantph.F90 (unit = 23, file = 'test.cpin')
Fortran runtime error: Cannot match namelist object name 0.090.09-0.180.090.09-0.180.090.09-0.180.09
-----------------------------------------------------
The mdout file ends at the same place as before:
----------------------------------------------------------
Implicit solvent radii are ArgH and AspGluO modified Bondi2 radii (mbondi3)
|reading charge increments from file: test.cpin
-----------------------------------------------------------
>From the error message above (Cannot match namelist object name 0.090.09-0.180.090.09-0.180.090.09-0.180.09), it seems there is a problem recognizing some of the commas between atom charges when reading in the cpin file. I have double checked that the commas are all present in the original cpin file (included with this email). The group I am titrating is a phosphate group, with three possible protonation sites (on on each oxygen). I first tested the residue definition and finddgref.py with only one protonation site, and was able to calculate the reference energy and run CpH simulation without error. After running into this problem with the 3-site definition, I went back and tried with just 2 possible protonation sites. Again, the simulation ran without problem. Finally, I tried with three protonation states defined, but the second two were just identical copies of the first one (this was to determine if there was a problem with the third state I had defined, since 1 and 1/2 ran fine, but 1/2/3 gave the above error). This simulation also failed with the same error as above ("Fortran runtime error: Cannot match namelist object name 0.090.09-0.180.090.09-0.180.090.09-0.180.09").
I have included the following cpin files with this email:
3_site.cpin - the original cpin file with protonation sites on all three phosphate oxygens (the one I'd ultimately like to use) - 4 states total - simulation fails
1_site.cpin - residue definition with just one oxygen protonation site - 2 states total - simulation runs
2_site.cpin - protonation possible on two unique oxygen atoms - 3 states total - simulation runs
3_site_copy.cpin - 3 protonation states but all 3 are identical copies of the one in "1_state.cpin" - 4 states total - simulation fails
There seems to only be a problem reading in the cpin file with any 3-site definition, which suggests to me the issue is related to the length of the cpin file or number of states defined, rather than an error with the cpin itself. Does anyone have any insight into this problem?
Thank you for the help,
Amy
--
Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology
--
Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology
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Received on Thu Nov 01 2018 - 13:00:03 PDT
