On Sun, Mar 24, 2013 at 6:42 AM, spin <[email protected]> wrote: > Hello, everyone, > I have tried to create a mutant of CYS, the CYC, which the S was > replaced with a C at the end of its side chain. After using pdb2gmx to > build > the .top file, I added bond and nonbond parameters to link the side chain > of > two CYC as the disulfide bond for CYS. Also all necessary force field > parameters have been added, especially those in ffbonded.itp and > ffnonbond.itp. But when I use grompp, it give the following information: > /ERROR 1 [file TP-2.top, line 421]: > No default Bond types/ >
There's a contradiction somewhere. If "necessary parameters have been added" then grompp would not find something to complain about on line 421. What's there? Are your #includes referring to the forcefield files you think they are? Mark > There are 45 errors like this. The atom types of the side chain of CYC > are > described by GCenFF and those of the main chain are described by CHARMM. > There are bond types, angle types and dihedral types of atoms from both the > main side and the side chain. I created them just by replace the CHARMM > atom > types with GCenFF atom types of the side chain. For example, the angle type > *HB CT2 CT1* was replaced with *HGA2 CG321 CT1*. > Later I found that there were angle types and dihedral types in .top file > missed in ffbonded.itp for both CYS and CYC. The topology of CYS can be > recognized normally by grompp, while the one of CYC can not. Can someone > tell me the reason? > > Thank you! > > Qing Liu > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/A-problem-of-adding-new-bond-parameters-tp5006580.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
