Hello Vinicius,
Yes, I ran at 6 different redox potentials, but truncated the output in my original message. Below is the entirety of what I am piping to fitpkaeo.py.
Redox potential is -0.03000 V, temperature is 300.00 K
HEH 1268: Offset -0.13262 V Pred Eo -0.16262 V Frac Redu 0.00588 Transitions 840
HEH 1271: Offset -0.22268 V Pred Eo -0.25268 V Frac Redu 0.00018 Transitions 26
HEH 1274: Offset -0.17568 V Pred Eo -0.20568 V Frac Redu 0.00112 Transitions 160
HEH 1277: Offset -0.16433 V Pred Eo -0.19433 V Frac Redu 0.00173 Transitions 248
HEH 1280: Offset -0.06561 V Pred Eo -0.09561 V Frac Redu 0.07324 Transitions 7284
HEH 1283: Offset -0.22268 V Pred Eo -0.25268 V Frac Redu 0.00018 Transitions 26
HEH 1286: Offset -0.08489 V Pred Eo -0.11489 V Frac Redu 0.03614 Transitions 4936
HEH 1289: Offset -0.19174 V Pred Eo -0.22174 V Frac Redu 0.00060 Transitions 86
HEH 1292: Offset -0.15631 V Pred Eo -0.18631 V Frac Redu 0.00236 Transitions 338
HEH 1295: Offset -0.17877 V Pred Eo -0.20877 V Frac Redu 0.00099 Transitions 142
HEH 1298: Offset -0.11424 V Pred Eo -0.14424 V Frac Redu 0.01190 Transitions 1626
HEH 1301: Offset -0.21028 V Pred Eo -0.24028 V Frac Redu 0.00029 Transitions 42
HEH 1304: Offset -0.15182 V Pred Eo -0.18182 V Frac Redu 0.00281 Transitions 402
HEH 1307: Offset -0.18585 V Pred Eo -0.21585 V Frac Redu 0.00075 Transitions 108
HEH 1310: Offset -0.20105 V Pred Eo -0.23105 V Frac Redu 0.00042 Transitions 60
HEH 1313: Offset -0.15855 V Pred Eo -0.18855 V Frac Redu 0.00217 Transitions 310
HEH 1316: Offset -0.13598 V Pred Eo -0.16598 V Frac Redu 0.00517 Transitions 740
HEH 1319: Offset -0.17701 V Pred Eo -0.20701 V Frac Redu 0.00106 Transitions 152
Average total molecular reduction: 36.14699
Redox potential is -0.09000 V, temperature is 300.00 K
HEH 1268: Offset -0.07337 V Pred Eo -0.16337 V Frac Redu 0.05530 Transitions 5714
HEH 1271: Offset -0.16675 V Pred Eo -0.25675 V Frac Redu 0.00158 Transitions 192
HEH 1274: Offset -0.12245 V Pred Eo -0.21245 V Frac Redu 0.00869 Transitions 1058
HEH 1277: Offset -0.10420 V Pred Eo -0.19420 V Frac Redu 0.01745 Transitions 2064
HEH 1280: Offset -0.00896 V Pred Eo -0.09896 V Frac Redu 0.41420 Transitions 15317
HEH 1283: Offset -0.16141 V Pred Eo -0.25141 V Frac Redu 0.00194 Transitions 236
HEH 1286: Offset -0.00084 V Pred Eo -0.09084 V Frac Redu 0.49183 Transitions 24234
HEH 1289: Offset -0.15890 V Pred Eo -0.24890 V Frac Redu 0.00214 Transitions 260
HEH 1292: Offset -0.14433 V Pred Eo -0.23433 V Frac Redu 0.00375 Transitions 456
HEH 1295: Offset -0.12689 V Pred Eo -0.21689 V Frac Redu 0.00733 Transitions 888
HEH 1298: Offset -0.05336 V Pred Eo -0.14336 V Frac Redu 0.11266 Transitions 8434
HEH 1301: Offset -0.12701 V Pred Eo -0.21701 V Frac Redu 0.00730 Transitions 828
HEH 1304: Offset -0.05463 V Pred Eo -0.14463 V Frac Redu 0.10783 Transitions 10690
HEH 1307: Offset -0.12784 V Pred Eo -0.21784 V Frac Redu 0.00707 Transitions 860
HEH 1310: Offset -0.14456 V Pred Eo -0.23456 V Frac Redu 0.00371 Transitions 450
HEH 1313: Offset -0.10923 V Pred Eo -0.19923 V Frac Redu 0.01441 Transitions 1722
HEH 1316: Offset -0.09772 V Pred Eo -0.18772 V Frac Redu 0.02232 Transitions 2700
HEH 1319: Offset -0.13756 V Pred Eo -0.22756 V Frac Redu 0.00486 Transitions 592
Average total molecular reduction: 37.28436
Redox potential is -0.15000 V, temperature is 300.00 K
HEH 1268: Offset 0.01560 V Pred Eo -0.13440 V Frac Redu 0.64641 Transitions 19185
HEH 1271: Offset -0.13466 V Pred Eo -0.28466 V Frac Redu 0.00544 Transitions 622
HEH 1274: Offset -0.06002 V Pred Eo -0.21002 V Frac Redu 0.08935 Transitions 9620
HEH 1277: Offset -0.05903 V Pred Eo -0.20903 V Frac Redu 0.09252 Transitions 8710
HEH 1280: Offset 0.08177 V Pred Eo -0.06823 V Frac Redu 0.95942 Transitions 3890
HEH 1283: Offset -0.14515 V Pred Eo -0.29515 V Frac Redu 0.00363 Transitions 420
HEH 1286: Offset 0.03444 V Pred Eo -0.11556 V Frac Redu 0.79123 Transitions 14981
HEH 1289: Offset -0.12689 V Pred Eo -0.27689 V Frac Redu 0.00733 Transitions 824
HEH 1292: Offset -0.08661 V Pred Eo -0.23661 V Frac Redu 0.03389 Transitions 3870
HEH 1295: Offset -0.05760 V Pred Eo -0.20760 V Frac Redu 0.09727 Transitions 9120
HEH 1298: Offset 0.04212 V Pred Eo -0.10788 V Frac Redu 0.83608 Transitions 10395
HEH 1301: Offset -0.09190 V Pred Eo -0.24190 V Frac Redu 0.02779 Transitions 3110
HEH 1304: Offset -0.01036 V Pred Eo -0.16036 V Frac Redu 0.40112 Transitions 20430
HEH 1307: Offset -0.08284 V Pred Eo -0.23284 V Frac Redu 0.03900 Transitions 4056
HEH 1310: Offset -0.10194 V Pred Eo -0.25194 V Frac Redu 0.01902 Transitions 2200
HEH 1313: Offset -0.04595 V Pred Eo -0.19595 V Frac Redu 0.14461 Transitions 12202
HEH 1316: Offset -0.03746 V Pred Eo -0.18746 V Frac Redu 0.19013 Transitions 17462
HEH 1319: Offset -0.10121 V Pred Eo -0.25121 V Frac Redu 0.01955 Transitions 2210
Average total molecular reduction: 40.40379
Redox potential is -0.21000 V, temperature is 300.00 K
HEH 1268: Offset 0.02964 V Pred Eo -0.18036 V Frac Redu 0.75887 Transitions 16357
HEH 1271: Offset -0.09059 V Pred Eo -0.30059 V Frac Redu 0.02920 Transitions 2619
HEH 1274: Offset -0.04804 V Pred Eo -0.25804 V Frac Redu 0.13491 Transitions 10068
HEH 1277: Offset 0.03056 V Pred Eo -0.17944 V Frac Redu 0.76531 Transitions 12879
HEH 1280: Offset 0.12553 V Pred Eo -0.08447 V Frac Redu 0.99228 Transitions 782
HEH 1283: Offset -0.10751 V Pred Eo -0.31751 V Frac Redu 0.01539 Transitions 1572
HEH 1286: Offset 0.09274 V Pred Eo -0.11726 V Frac Redu 0.97307 Transitions 2620
HEH 1289: Offset -0.07285 V Pred Eo -0.28285 V Frac Redu 0.05637 Transitions 4782
HEH 1292: Offset -0.04982 V Pred Eo -0.25982 V Frac Redu 0.12708 Transitions 10552
HEH 1295: Offset -0.00344 V Pred Eo -0.21344 V Frac Redu 0.46674 Transitions 19579
HEH 1298: Offset 0.08964 V Pred Eo -0.12036 V Frac Redu 0.96974 Transitions 2748
HEH 1301: Offset -0.03157 V Pred Eo -0.24157 V Frac Redu 0.22775 Transitions 16531
HEH 1304: Offset 0.05346 V Pred Eo -0.15654 V Frac Redu 0.88775 Transitions 9042
HEH 1307: Offset -0.03960 V Pred Eo -0.24960 V Frac Redu 0.17771 Transitions 11382
HEH 1310: Offset -0.05097 V Pred Eo -0.26097 V Frac Redu 0.12220 Transitions 9761
HEH 1313: Offset 0.00554 V Pred Eo -0.20446 V Frac Redu 0.55336 Transitions 18176
HEH 1316: Offset 0.03655 V Pred Eo -0.17345 V Frac Redu 0.80435 Transitions 16262
HEH 1319: Offset -0.06458 V Pred Eo -0.27458 V Frac Redu 0.07600 Transitions 7726
Average total molecular reduction: 44.13807
Redox potential is -0.27000 V, temperature is 300.00 K
HEH 1268: Offset 0.09714 V Pred Eo -0.17286 V Frac Redu 0.97719 Transitions 2222
HEH 1271: Offset -0.02900 V Pred Eo -0.29900 V Frac Redu 0.24570 Transitions 15080
HEH 1274: Offset 0.00610 V Pred Eo -0.26390 V Frac Redu 0.55871 Transitions 21971
HEH 1277: Offset 0.03789 V Pred Eo -0.23211 V Frac Redu 0.81240 Transitions 11366
HEH 1280: Offset 0.18058 V Pred Eo -0.08942 V Frac Redu 0.99908 Transitions 106
HEH 1283: Offset -0.02286 V Pred Eo -0.29286 V Frac Redu 0.29229 Transitions 20637
HEH 1286: Offset 0.14059 V Pred Eo -0.12941 V Frac Redu 0.99567 Transitions 494
HEH 1289: Offset -0.02135 V Pred Eo -0.29135 V Frac Redu 0.30456 Transitions 17117
HEH 1292: Offset -0.01034 V Pred Eo -0.28034 V Frac Redu 0.40128 Transitions 19070
HEH 1295: Offset 0.03237 V Pred Eo -0.23763 V Frac Redu 0.77770 Transitions 12150
HEH 1298: Offset 0.12765 V Pred Eo -0.14235 V Frac Redu 0.99288 Transitions 790
HEH 1301: Offset 0.06059 V Pred Eo -0.20941 V Frac Redu 0.91244 Transitions 8708
HEH 1304: Offset 0.10575 V Pred Eo -0.16425 V Frac Redu 0.98355 Transitions 1832
HEH 1307: Offset -0.00115 V Pred Eo -0.27115 V Frac Redu 0.48891 Transitions 21374
HEH 1310: Offset -0.03312 V Pred Eo -0.30312 V Frac Redu 0.21735 Transitions 16024
HEH 1313: Offset 0.05849 V Pred Eo -0.21151 V Frac Redu 0.90572 Transitions 6958
HEH 1316: Offset 0.09426 V Pred Eo -0.17574 V Frac Redu 0.97458 Transitions 2908
HEH 1319: Offset 0.00260 V Pred Eo -0.26740 V Frac Redu 0.52512 Transitions 28072
Average total molecular reduction: 48.36513
Redox potential is -0.33000 V, temperature is 300.00 K
HEH 1268: Offset 0.13012 V Pred Eo -0.19988 V Frac Redu 0.99352 Transitions 784
HEH 1271: Offset 0.06241 V Pred Eo -0.26759 V Frac Redu 0.91789 Transitions 8879
HEH 1274: Offset 0.06628 V Pred Eo -0.26372 V Frac Redu 0.92850 Transitions 8288
HEH 1277: Offset 0.08485 V Pred Eo -0.24515 V Frac Redu 0.96381 Transitions 4034
HEH 1280: Offset 0.20601 V Pred Eo -0.12399 V Frac Redu 0.99965 Transitions 42
HEH 1283: Offset 0.04061 V Pred Eo -0.28939 V Frac Redu 0.82792 Transitions 15342
HEH 1286: Offset 0.15883 V Pred Eo -0.17117 V Frac Redu 0.99786 Transitions 260
HEH 1289: Offset 0.07972 V Pred Eo -0.25028 V Frac Redu 0.95622 Transitions 5035
HEH 1292: Offset 0.06086 V Pred Eo -0.26914 V Frac Redu 0.91326 Transitions 9047
HEH 1295: Offset 0.08115 V Pred Eo -0.24885 V Frac Redu 0.95848 Transitions 4608
HEH 1298: Offset 0.17206 V Pred Eo -0.15794 V Frac Redu 0.99871 Transitions 156
HEH 1301: Offset 0.12108 V Pred Eo -0.20892 V Frac Redu 0.99084 Transitions 1112
HEH 1304: Offset 0.17486 V Pred Eo -0.15514 V Frac Redu 0.99885 Transitions 140
HEH 1307: Offset 0.10226 V Pred Eo -0.22774 V Frac Redu 0.98122 Transitions 2256
HEH 1310: Offset 0.04659 V Pred Eo -0.28341 V Frac Redu 0.85842 Transitions 14754
HEH 1313: Offset 0.08178 V Pred Eo -0.24822 V Frac Redu 0.95943 Transitions 4604
HEH 1316: Offset 0.14426 V Pred Eo -0.18574 V Frac Redu 0.99624 Transitions 456
HEH 1319: Offset 0.08567 V Pred Eo -0.24433 V Frac Redu 0.96490 Transitions 4170
Average total molecular reduction: 53.20574
Redox potential is -0.39000 V, temperature is 300.00 K
HEH 1268: Offset 0.18261 V Pred Eo -0.20739 V Frac Redu 0.99915 Transitions 124
HEH 1271: Offset 0.10374 V Pred Eo -0.28626 V Frac Redu 0.98224 Transitions 2558
HEH 1274: Offset 0.12977 V Pred Eo -0.26023 V Frac Redu 0.99344 Transitions 952
HEH 1277: Offset 0.14185 V Pred Eo -0.24815 V Frac Redu 0.99588 Transitions 598
HEH 1280: Offset 0.27141 V Pred Eo -0.11859 V Frac Redu 0.99997 Transitions 4
HEH 1283: Offset 0.10951 V Pred Eo -0.28049 V Frac Redu 0.98574 Transitions 2016
HEH 1286: Offset 0.22301 V Pred Eo -0.16699 V Frac Redu 0.99982 Transitions 26
HEH 1289: Offset 0.11709 V Pred Eo -0.27291 V Frac Redu 0.98933 Transitions 1548
HEH 1292: Offset 0.12517 V Pred Eo -0.26483 V Frac Redu 0.99217 Transitions 1130
HEH 1295: Offset 0.13410 V Pred Eo -0.25590 V Frac Redu 0.99444 Transitions 806
HEH 1298: Offset 0.22733 V Pred Eo -0.16267 V Frac Redu 0.99985 Transitions 22
HEH 1301: Offset 0.20941 V Pred Eo -0.18059 V Frac Redu 0.99970 Transitions 44
HEH 1304: Offset 0.18977 V Pred Eo -0.20023 V Frac Redu 0.99935 Transitions 94
HEH 1307: Offset 0.14518 V Pred Eo -0.24482 V Frac Redu 0.99637 Transitions 524
HEH 1310: Offset 0.11750 V Pred Eo -0.27250 V Frac Redu 0.98949 Transitions 1524
HEH 1313: Offset 0.12668 V Pred Eo -0.26332 V Frac Redu 0.99261 Transitions 1070
HEH 1316: Offset 0.23902 V Pred Eo -0.15098 V Frac Redu 0.99990 Transitions 14
HEH 1319: Offset 0.13265 V Pred Eo -0.25735 V Frac Redu 0.99413 Transitions 852
Average total molecular reduction: 53.90357
Best,
Matthew
> On Jul 17, 2021, at 9:17 PM, Cruzeiro, Vinicius <vcruzeiro.UCSD.EDU> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> Hello Matthew,
>
> Your output from cestats seems to be for a single redox value, is this correct? If so, you need to have more redox potential values for the fitting.
>
> Best,
>
> Vinícius Wilian D. Cruzeiro, PhD
> Postdoctoral Researcher
> San Diego Supercomputer Center
> Department of Chemistry and Biochemistry
> University of California, San Diego
> Voice: +1(858)246-5584
> Twitter: .vwcruzeiro
> ________________________________
> From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
> Sent: Saturday, July 17, 2021 3:40 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] fitpkaeo.py not reading input from cestats
>
> Dear Amber Community,
>
> fitpkaeo.py is not working for output from cestats like the below. I was able to figure out that fitpkaeo.py is not parsing the input stream correctly, and thinks there are zero residues. When I tinker with the code, I can get it to recognize that there are 18 residues, but then it doesn’t parse the lines correctly to get the Frac Redu. Can someone please help with how the code needs to be modified?
>
> HEH 1268: Offset -0.13262 V Pred Eo -0.16262 V Frac Redu 0.00588 Transitions 840
> HEH 1271: Offset -0.22268 V Pred Eo -0.25268 V Frac Redu 0.00018 Transitions 26
> HEH 1274: Offset -0.17568 V Pred Eo -0.20568 V Frac Redu 0.00112 Transitions 160
> HEH 1277: Offset -0.16433 V Pred Eo -0.19433 V Frac Redu 0.00173 Transitions 248
> HEH 1280: Offset -0.06561 V Pred Eo -0.09561 V Frac Redu 0.07324 Transitions 7284
> HEH 1283: Offset -0.22268 V Pred Eo -0.25268 V Frac Redu 0.00018 Transitions 26
> HEH 1286: Offset -0.08489 V Pred Eo -0.11489 V Frac Redu 0.03614 Transitions 4936
> HEH 1289: Offset -0.19174 V Pred Eo -0.22174 V Frac Redu 0.00060 Transitions 86
> HEH 1292: Offset -0.15631 V Pred Eo -0.18631 V Frac Redu 0.00236 Transitions 338
> HEH 1295: Offset -0.17877 V Pred Eo -0.20877 V Frac Redu 0.00099 Transitions 142
> HEH 1298: Offset -0.11424 V Pred Eo -0.14424 V Frac Redu 0.01190 Transitions 1626
> HEH 1301: Offset -0.21028 V Pred Eo -0.24028 V Frac Redu 0.00029 Transitions 42
> HEH 1304: Offset -0.15182 V Pred Eo -0.18182 V Frac Redu 0.00281 Transitions 402
> HEH 1307: Offset -0.18585 V Pred Eo -0.21585 V Frac Redu 0.00075 Transitions 108
> HEH 1310: Offset -0.20105 V Pred Eo -0.23105 V Frac Redu 0.00042 Transitions 60
> HEH 1313: Offset -0.15855 V Pred Eo -0.18855 V Frac Redu 0.00217 Transitions 310
> HEH 1316: Offset -0.13598 V Pred Eo -0.16598 V Frac Redu 0.00517 Transitions 740
> HEH 1319: Offset -0.17701 V Pred Eo -0.20701 V Frac Redu 0.00106 Transitions 152
>
> Best,
> Matthew
> _______________________________________________
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Received on Sat Jul 17 2021 - 18:30:02 PDT
