On 4/17/17 3:24 AM, Yogendra Patel wrote:
Hello gromacs users, I made a force field (rtp) file for my polymer using CHARRM 27 in gromacs 4.5.5. While running the pdb2gmx to generate the topology, I'm getting the error as follows. I have kept the modified rtp file, pdb file and modified ffbonded.itp file in my working folder. The rtp file has been named as
Then that's your problem. Files in the working directory are not being read, instead you are reading everything out of $GMXLIB/charmm27.ff, as the pdb2gmx output notes. If you want to modify force field files locally, you must create an entire force field directory, modify the files within it, then choose that directory when prompted by pdb2gmx.
-Justin
aminoacids.rtp same as mentioned in gromacs top folder .Please suggest and help. Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.r2b Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.r2b Reading i-paa@30_2.pdb... Read 257 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 30 residues with 257 atoms chain #res #atoms 1 ' ' 30 257 All occupancies are one Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/atomtypes.atp Atomtype 1 Reading residue database... (charmm27) Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.rtp Residue 43 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.rtp Residue 47 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.rtp Residue 59 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.rtp Residue 63 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.c.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.c.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.c.tdb Back Off! I just backed up topol.top to ./#topol.top.10# Processing chain 1 (257 atoms, 30 residues) Identified residue PAHb1 as a starting terminus. Identified residue PAHe30 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully ------------------------------------------------------- Program pdb2gmx, VERSION 4.5.5 Source code file: resall.c, line: 581 Fatal error: Residue 'PAHb' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -------------------------------------------------------
-- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
