Re: [gmx-users] Error in DNA.itp file
On 11/5/19 11:55 AM, Najamuddin Memon wrote: You may use Amber99sb force field for DNA-protein simulation and also put residue type.dat file in your folder. It will work The nucleic acid parameter sets packaged with these GROMACS ports are wildly outdated. I suggest finding better parameters from other sources. People have ported AMBER parameters, though they should be checked thoroughly. -Justin On Tue, Nov 5, 2019, 6:59 PM Paul bauer wrote: Hello, the error states that you are missing parameters for your system. Did you check that the forcefield contains all the special parameters you need for the conjugate molecule? Also, I would recommend to not use a prehistoric version of GROMACS for new studies, if there are no specific reasons preventing you from using a more recent one that is still supported (such as 2018 or 2019). Cheers Paul On 05/11/2019 14:47, Ayesha Kanwal wrote: 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 -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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. -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Error in DNA.itp file
Residue type.dat file having definition of nucleotides On Tue, Nov 5, 2019, 9:55 PM Najamuddin Memon wrote: > You may use Amber99sb force field for DNA-protein simulation and also put > residue type.dat file in your folder. It will work > > > On Tue, Nov 5, 2019, 6:59 PM Paul bauer wrote: > >> Hello, >> >> the error states that you are missing parameters for your system. Did >> you check that the forcefield contains all the special parameters you >> need for the conjugate molecule? >> Also, I would recommend to not use a prehistoric version of GROMACS for >> new studies, if there are no specific reasons preventing you from using >> a more recent one that is still supported (such as 2018 or 2019). >> >> Cheers >> >> Paul >> >> On 05/11/2019 14:47, Ayesha Kanwal wrote: >> > 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 >> > >> > >> >> -- >> Paul Bauer, PhD >> GROMACS Release Manager >> KTH Stockholm, SciLifeLab >> 0046737308594 >> >> -- >> 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.
Re: [gmx-users] Error in DNA.itp file
You may use Amber99sb force field for DNA-protein simulation and also put residue type.dat file in your folder. It will work On Tue, Nov 5, 2019, 6:59 PM Paul bauer wrote: > Hello, > > the error states that you are missing parameters for your system. Did > you check that the forcefield contains all the special parameters you > need for the conjugate molecule? > Also, I would recommend to not use a prehistoric version of GROMACS for > new studies, if there are no specific reasons preventing you from using > a more recent one that is still supported (such as 2018 or 2019). > > Cheers > > Paul > > On 05/11/2019 14:47, Ayesha Kanwal wrote: > > 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 > > > > > > -- > Paul Bauer, PhD > GROMACS Release Manager > KTH Stockholm, SciLifeLab > 0046737308594 > > -- > 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.
Re: [gmx-users] Error in DNA.itp file
Hello, the error states that you are missing parameters for your system. Did you check that the forcefield contains all the special parameters you need for the conjugate molecule? Also, I would recommend to not use a prehistoric version of GROMACS for new studies, if there are no specific reasons preventing you from using a more recent one that is still supported (such as 2018 or 2019). Cheers Paul On 05/11/2019 14:47, Ayesha Kanwal wrote: 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 -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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.
