[gmx-users] Error in DNA.itp file
Hi all, i am preparing system of DNA-protein complex, downloaded it from RCSB website, by using GROMACS-version 4.5.5; force field AMBER03WS with water Model TIP4P (2005). The DNA chain contains DA, DT, DG, DC atom type. but the problem is that when i use command for energy minimization the following error has occurred. Error shows that problem is in .itp file Dih. types. For protein .itp files,there was no problem. Only DNA .itp files have issue. Its my first time i am preparing this kind of system please let me know how can i resolve this problem and why these errors were generated ? I have searched out previous mail but could not find relevant answer so i am posting it now here. i have attached .mdp file with this e-mail. checking input for internal consistency... Generated 2412 of the 2415 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2415 of the 2415 1-4 parameter combinations ERROR 1 [file dna-his_DNA_chain_I.itp, line 44148]: No default Improper Dih. types ERROR 2 [file dna-his_DNA_chain_J.itp, line 44148]: No default Improper Dih. types -- 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] (no subject)
Hi all, i am preparing system of DNA-protein complex, downloaded it from RCSB website, by using GROMACS force field AMBER03WS with water Model TIP4P (2005). The DNA chain contains DA, DT, DG, DC atom type. but the problem is that when i use command for energy minimization the following error has occurred. Error shows that problem is in .itp file Dih. types. Its my first time i am preparing this kind of system please let me know how can i resolve this problem and why this error generated ? I have searched out previous mail but could not find relevant answer so i am posting it now here. i have attached .mdp file with this e-mail. checking input for internal consistency... Generated 2412 of the 2415 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2415 of the 2415 1-4 parameter combinations ERROR 1 [file dna-his_DNA_chain_I.itp, line 44148]: No default Improper Dih. types ERROR 2 [file dna-his_DNA_chain_J.itp, line 44148]: No default Improper Dih. types -- 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] Free energy calculation of Histone
Dear all users, I am new for using GROMACS. and also read the tutorial of Methane and water. I have already simulated data of 100 ns for four histones. I want to know how to calculate free energy solvation from this data. which topology file and coordinate files I will use? I will appreciate your good suggestions. Regards Ayesha -- 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] free energy calculation for histone
Dear all users, I am new for using GROMACS. and also read the tutorial of Methane and water. I have already simulated data of 100 ns for four histones. I want to know how to calculate free energy solvation from this data. which topology file and coordinate files I will use? I will appreciate your good suggestions. Regards Ayesha Kanwal -- 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.
Re: [gmx-users] how to make .trr file readable
Dear Bipin Singh, i had read MDAnalysis but i could not get it to how make .trr file readable . could you provide me an easy tutorial ? or number of steps to which i can easily follow it and make .trr readable. or there is any source code which i can use for reading this file. > Date: Tue, 1 Dec 2015 18:17:49 +0530 > From: bipinel...@gmail.com > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] how to make .trr file readable > > http://pythonhosted.org/MDAnalysis/documentation_pages/coordinates/TRR.html > > > -- > Thanks and Regards, > Bipin Singh > > On Tue, Dec 1, 2015 at 6:10 PM, Ayesha Kanwal > wrote: > > > Dear Gromacs experts, > > i am very new to Gromacs i only want to take .trr file and make it > > readable . as i want to use .trr file in my own tool as an input format. > > how can i make it readable and can use it in my tool ? > > Best regards > > Ayesha > > > > -- > > 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. > > > -- > 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. -- 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 make .trr file readable
Dear Gromacs experts, i am very new to Gromacs i only want to take .trr file and make it readable . as i want to use .trr file in my own tool as an input format. how can i make it readable and can use it in my tool ? Best regards Ayesha -- 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] about .trr input file format
hi , i want to use .trr file format in my tool for reading input .trr file and analyze how can i use it in my GUI based tool ? or any one who can guide me how can i use .trr file for analyzing PCA, CrossCorrelation , Entropy and Enthalpy MMPBSA/GBSA . i already using AMBERtool "MMPBSA.py for the calculation of enthalpy and using DCD file format but now i also want to provide .trr file format , i.e my tool can read .trr file and give same output like DCD file gives in a 2D graph form. -- 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.
