1] I created Diglycine peptide from chimera software, and got the .pdb file, added two different solvents (A, B) and made two different systems say, A-(Diglycine+solvent1), B-(Diglycine+solvent2). I generated the topology file from charmm36 FF by gmx pdb2gmx process for both the systems A and B correctly (but in system A there is no [ cmap ] line in topology, but system B has [ cmap ] in topology).. Why is this in one system i am getting but in other i am not..? Is there any error...or what is it...
2] And during gmx grompp -f min.mdp -c mixture.gro -p topol.top -o min.tpr for system A (whr there is no [cmap] in topology), the gmx grompp command works well... But for system B (which has [cmap] in topology), the error comes as:- > ERROR 1 [file topol.top, line 8231]: > Unknown cmap torsion between atoms 8 10 12 15 18 How can i solve this ...?? Thank you... On Mon, Aug 21, 2017 at 10:18 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Mon, Aug 21, 2017 at 6:33 PM Dilip H N <cy16f01.di...@nitk.edu.in> > wrote: > > > Hello, > > I have created a peptide from chimera software and got the pdb file, and > i > > have added solvents to it the resultant is mixture.gro, and used gmx > > pdb2gmx to generate the topology using charmm36 FF. I got the topology > > correct, but nw if i give the command for energy minimization :- > > gmx grompp -f min.mdp -c mixture.gro -p topol.top -o min.tpr > > > > I am getting error as:- > > > > NOTE 1 [file min.mdp]: > > With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note > > that with the Verlet scheme, nstlist has no effect on the accuracy of > > your simulation. > > > > Setting the LD random seed to -1490567170 > > Generated 97877 of the 97903 non-bonded parameter combinations > > Generating 1-4 interactions: fudge = 1 > > Generated 64492 of the 97903 1-4 parameter combinations > > > > ERROR 1 [file topol.top, line 8231]: > > Unknown cmap torsion between atoms 8 10 12 15 18 > > > > There was 1 note > > ------------------------------------------------------- > > Program: gmx grompp, version 2016.3 > > Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1622) > > > > Fatal error: > > There was 1 error in input file(s) > > > > 1] What is this cmap all about..?? > > > > That's part of how the CHARMM force field works for modelling peptides. You > should have a basic understanding of that from your background reading that > led to the choice of this force field. > > > > 2] How do i correct this error..? > > > > Whether you can do so depends whether chimera has generated a structure > that has a valid CHARMM36 representation, ie there exists a CMAP definition > for the types of those atoms. > > Mark > > > > Any suggestions will be helpful... > > > > Thank you... > > > > > > > > > > -- > > With Best Regards, > > > > DILIP.H.N > > Ph.D Student > > -- > > 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. > -- With Best Regards, DILIP.H.N Ph.D Student -- 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.