[gmx-users] alchemical_analysis IndexError
Dear all,
I am doing thermodynamic integration and I am analysing my data using the
alchemical_analysis scrip which I successfully installed, when I run I am
getting this error, Please assist how to resolve this issue.
Traceback (most recent call last):
File "/usr/local/bin/alchemical_analysis", line 11, in
load_entry_point('alchemical-analysis==1.0.2.dev0', 'console_scripts',
'alchemical_analysis')()
File
"/usr/local/lib/python2.7/dist-packages/alchemical_analysis-1.0.2.dev0-py2.7.egg/alchemical_analysis/alchemical_analysis.py",
line 1222, in main
nsnapshots, lv, dhdlt, u_klt = parser_gromacs.readDataGromacs(P)
File
"/usr/local/lib/python2.7/dist-packages/alchemical_analysis-1.0.2.dev0-py2.7.egg/alchemical_analysis/parser_gromacs.py",
line 324, in readDataGromacs
nsnapshots[nf,nf] += unixlike.wcPy(f.filename) - f.skip_lines -
1*bLenConsistency
IndexError: index 20 is out of bounds for axis 1 with size 20
--
*Regards, *
Daniel Madulu Shadrack., (M.Sc. Chem).
PhD Research Scholar
(Nanomedicine & Comp. Aided Drug Design)
dmss...@gmail.com
-
*FOR GOD LET US DO MUCH, **QUICK AND **WELL*..
*St. Gaspar Del Bufalo*
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[gmx-users] Positive free energy from Thermodynamics integration
Dear All, I am performing TI using gromacs for two system i.e receptor and ligand. Here the receptor is a polymer i.e chitosan but I am getting + 115 +/-0.9 kJ/mol. The final results are here below and I have attached my sample input files. Please assist, is correct to get this energy? should I assume that the reverse reaction is negative? Or what is my problem in my input files? I am calculating using bar module. Temperature: 300 K Detailed results in kT (see help for explanation): lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/- 0 19.60 0.322.22 0.331.89 0.262.32 0.19 1 26.24 0.151.47 0.181.34 0.171.83 0.10 2 33.33 0.101.57 0.121.40 0.111.83 0.08 3 40.83 0.111.09 0.041.04 0.041.50 0.03 4 52.73 0.040.25 0.080.31 0.100.64 0.03 5 62.67 0.060.06 0.070.08 0.070.58 0.01 6 75.49 0.030.57 0.040.80 0.031.16 0.01 7 85.34 0.070.64 0.060.90 0.071.23 0.03 8 95.12 0.060.70 0.070.99 0.171.45 0.04 9 104.62 0.071.11 0.121.52 0.101.58 0.06 10 114.07 0.120.98 0.041.46 0.091.72 0.03 11 121.73 0.040.49 0.040.55 0.030.93 0.01 12 131.52 0.080.37 0.050.49 0.060.99 0.02 13 141.10 0.100.67 0.060.92 0.081.25 0.04 14 15 -0.30 0.131.47 0.142.13 0.201.98 0.11 15 16 -2.67 0.181.78 0.141.66 0.142.04 0.10 16 17 -2.89 0.060.53 0.080.43 0.040.99 0.04 17 18 -1.77 0.010.18 0.010.17 0.010.57 0.01 18 19 -0.57 0.010.08 0.010.09 0.010.42 0.01 Final results in kJ/mol: point 0 - 1, DG 23.94 +/- 0.80 point 1 - 2, DG 15.56 +/- 0.37 point 2 - 3, DG 8.29 +/- 0.24 point 3 - 4, DG 2.07 +/- 0.28 point 4 - 5, DG 6.82 +/- 0.11 point 5 - 6, DG 6.66 +/- 0.14 point 6 - 7, DG 13.69 +/- 0.07 point 7 - 8, DG 13.32 +/- 0.18 point 8 - 9, DG 12.78 +/- 0.14 point 9 - 10, DG 11.53 +/- 0.16 point 10 - 11, DG 10.15 +/- 0.30 point 11 - 12, DG 4.33 +/- 0.11 point 12 - 13, DG 3.79 +/- 0.20 point 13 - 14, DG 2.74 +/- 0.24 point 14 - 15, DG -0.74 +/- 0.32 point 15 - 16, DG -6.65 +/- 0.45 point 16 - 17, DG -7.22 +/- 0.15 point 17 - 18, DG -4.42 +/- 0.02 point 18 - 19, DG -1.42 +/- 0.02 total 0 - 19, DG 115.21 +/- 0.94 gcq#404: "Humbug! Most things free-born will submit to anything for a salary" (Mr. Rochester in Jane Eyre by Charlotte Bronte) Thank you for your help -- *Regards, * Daniel Madulu Shadrack., (M.Sc. Chem). PhD Research Scholar (Nanomedicine & Comp. Aided Drug Design) dmss...@gmail.com - *FOR GOD LET US DO MUCH, **QUICK AND **WELL*.. *St. Gaspar Del Bufalo* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] error in calculating free energy of solvation
Hi all, I am calculating the free energy of solvation in gromacs but I get this error, please help, I have tried all the options without sucdcess. Fatal error: There is no path between the states X & Y below that is covered by foreign lambdas: cannot proceed with BAR. Use thermodynamic integration of dH/dl by calculating the averages of dH/dl with g_analyze and integrating them. Alternatively, use the -extp option if (and only if) the Hamiltonian depends linearly on lambda, which is NOT normally the case. lambda vector [X]: init-lambda-state=3 (mass-lambda) l=0 (coul-lambda) l=0 (vdw-lambda) l=0.15 (bonded-lambda) l=0 (restraint-lambda) l=0 lambda vector [Y]: init-lambda-state=5 (mass-lambda) l=0 (coul-lambda) l=0 (vdw-lambda) l=0.25 (bonded-lambda) l=0 (restraint-lambda) l=0 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- *Regards, * Daniel Madulu Shadrack., (M.Sc. Chem). PhD Research Scholar (Nanomedicine & Comp. Aided Drug Design) dmss...@gmail.com - *FOR GOD LET US DO MUCH, **QUICK AND **WELL*.. *St. Gaspar Del Bufalo* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] RDF in gromacs
Hi, I am calculating the rdf of my system as follows. 1. rdf of oxygen atom of my drug and water this is successful (I just made an index file and for water i choose eg. 5 & a OW) this worked fine. 2. I want now to calculate the rdf of oxygen in my drug and oxygen from the hydroxyl group of the chitosan, I am getting difficult on how to select only oxygen in chitosan or polymer and make an index file, I am getting syntax errors, How should I do? Help. -- *Regards, * Daniel Madulu Shadrack., (M.Sc. Chem). PhD Research Scholar (Nanomedicine & Comp. Aided Drug Design) dmss...@gmail.com - *FOR GOD LET US DO MUCH, **QUICK AND **WELL*.. *St. Gaspar Del Bufalo* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Interaction energy, vdW and electrostatic
Hi all, I am simulating a polymer with drug (polymer-drug) complex, I want to plot the interaction energy. I use gmx energy -f xx.edr, I am getting a long list with kind of energy eg LJ-SR:polymer-polymer LJ-14:polymer-polymer LJ-SR:polymer-drug LJ-14:polymer-drug etc also I have Coul-SR:polymer-polymer Coul-14:polymer-polymer Coul-SR:polymer-drug Coul-14:polymer-drug etc So, is Coul-SR:polymer-drug stands for van der wall? and LJ-SR:polymer-drug stand for electrostaics? But when I use for example, LJ-14:polymer-drug I get zero, but when I use LJ-SR:polymer-drug I get -88.8 kJ/mol. Is this -88 the total interaction energy? how do I get the vdW and electrostatic to get the total interaction energy? Help -- *Regards, * Daniel Madulu Shadrack., (M.Sc. Chem). PhD Research Scholar (Nanomedicine & Comp. Aided Drug Design) dmss...@gmail.com - *FOR GOD LET US DO MUCH, **QUICK AND **WELL*.. *St. Gaspar Del Bufalo* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] combining multiple MD proteins,
Dear, I want to combine proteins to merge into single pdb but I get this error below. Command line: gmx trjcat -f 10ns.pdb 15ns.pdb 40ns.pdb 60ns.pdb 90ns.pdb -o all.pdb Reading frame 0 time 1.000'', 3420 atoms Last frame 0 time 1.000 Reading frame 0 time 15000.000'', 3420 atoms Last frame 0 time 15000.000 Reading frame 0 time 4.000'', 3420 atoms Last frame 0 time 4.000 Reading frame 0 time 6.000'', 3420 atoms Last frame 0 time 6.000 Reading frame 0 time 9.000'', 3420 atoms Last frame 0 time 9.000 Summary of files and start times used: FileStart time Time step - 10ns.pdb1.000 ps0.000 ps 15ns.pdb15000.000 ps0.000 ps 40ns.pdb4.000 ps0.000 ps 60ns.pdb6.000 ps0.000 ps 90ns.pdb9.000 ps0.000 ps Reading frame 0 time 1.000 Continue writing frames from 10ns.pdb t=1 ps, frame=0 --- Program gmx trjcat, VERSION 5.1.4 Source code file: /home/daniel/installed/gromacs-5.1.4/src/gromacs/fileio/trxio.c, line: 557 Fatal error: Can not write a pdb file without atom names For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- *Regards, * Daniel Madulu Shadrack., (M.Sc. Chem). PhD Research Scholar (Nanomedicine & Comp. Aided Drug Design) dmss...@gmail.com - *FOR GOD LET US DO MUCH, **QUICK AND **WELL*.. *St. Gaspar Del Bufalo* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to use ambconv
I all, I am using ambconv to convert and amber file to gromacs format but I get segment fault. Can anyone help me with the command may be. I checked in online but not successful. I am converting .prmtop and .incrd to gromacs .top and .gro -- *Regards, * Daniel Madulu Shadrack., (M.Sc. Chem). PhD Research Scholar (Nanomedicine & Comp. Aided Drug Design) dmss...@gmail.com - *FOR GOD LET US DO MUCH, **QUICK AND **WELL*.. *St. Gaspar Del Bufalo* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
