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 <[email protected]> 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 [email protected]. > -- 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 [email protected].
