Sorry I found this thread here: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-September/108197.html
>From my understanding, I use pdb2gmx on my entire output file, however, where does the data in the .psf file go? *Sanim Rahman* B.S. Chemical Engineering, 2019 Resident Assistant, Castor Hall Engineering Living Learning Community 2016-2017 Co-Founder and Co-President of the Undergraduate Research Society Undergraduate Researcher, Global Center for Hearing and Speech Research <https://www.linkedin.com/pub/sanim-rahman/108/a64/986> On Sat, Mar 18, 2017 at 12:37 AM, Sanim Rahman <san...@mail.usf.edu> wrote: > Hi all, > > I am trying to run grompp on POPC lipid bilayer that I constructed in > CHARMM-GUI. I originally input the whole assembled bilayer from CHARMM-GUI, > however, I received the error: > > "No Default U-B Types" > > From a few previous threads, it was suggested that I stripped the waters > and use pdb2gmx on them separately in GROMACS. I did that and included the > #include command in my lipid topology file to reference water.itp. However, > I receive the following error: > > "Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = > 1, > while at->nr = 17152)" > > This is what the end of my POPC topology file looks like: > > *; Include Position restraint file* > *#ifdef POSRES* > *#include "posre.itp"* > *#endif* > > *; Include water chain topology* > *#include "water.itp"* > > *; Include water topology* > *#include "./charmm36-nov2016.ff/tip3p.itp"* > > *#ifdef POSRES_WATER* > *; Position restraint for each water oxygen* > *[ position_restraints ]* > *; i funct fcx fcy fcz* > * 1 1 1000 1000 1000* > *#endif* > > *; Include topology for ions* > *#include "./charmm36-nov2016.ff/ions.itp"* > > *[ system ]* > *; Name* > *Protein* > > *[ molecules ]* > *; Compound #mols* > *Other 1* > *Water 1* > > I recalled implementing the same technique in one of the GROMACS tutorials, > but I am unsure what I am doing differently in my approach to receive this > error. > Thank you. I will truly appreciate your assistance. > *Sanim Rahman* > B.S. Chemical Engineering, 2019 > Resident Assistant, Castor Hall Engineering Living Learning Community > 2016-2017 > Co-Founder and Co-President of the Undergraduate Research Society > Undergraduate Researcher, Global Center for Hearing and Speech Research > <https://www.linkedin.com/pub/sanim-rahman/108/a64/986> > -- > 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.