Re: [gmx-users] Invalid atomtype format (Justin Lemkul
On 4/30/20 7:10 AM, Sadaf Rani wrote: Dear Justin I have removed the blank lines but getting a new warning while doing gmx pdb2gmx:- WARNING: Duplicate line found in or between hackblock and rtp entries I am not getting what else is wrong. Could you please help me to figure out. I have shared the file on the following link:- https://www.dropbox.com/s/c6tg9q4i0ara3vu/atomtypes.atp?dl=0 There's a lot to go through here with multiple ligands so I'm not going to be able to go through your files line-by-line. You have duplicate bond entries somewhere. Make your system simpler. Run *only* one ligand at a time through pdb2gmx to figure out which one is triggering the problem. Also note that you should remove the extraneous number 1 from all your [ bonds ] lines in your .rtp entries. They're going to lead to incorrect format in the resulting topology. Just specify the pairs of atoms that are bonded. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
Re: [gmx-users] Invalid atomtype format (Justin Lemkul
Dear Justin I have removed the blank lines but getting a new warning while doing gmx pdb2gmx:- WARNING: Duplicate line found in or between hackblock and rtp entries I am not getting what else is wrong. Could you please help me to figure out. I have shared the file on the following link:- https://www.dropbox.com/s/c6tg9q4i0ara3vu/atomtypes.atp?dl=0 Thanks. Sadaf -- 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.
Re: [gmx-users] Invalid atomtype format (Justin Lemkul)
On 4/29/20 7:41 PM, Sadaf Rani wrote: Dear Justin I have shared the files for the users mailing list on the following link. https://www.dropbox.com/s/bfaq8z8iqojdm0r/Atom_type_error%20files.zip?dl=0 Remove the blank lines from the end of atomtypes.atp and it works fine. Note that you should not be including LJ parameters in atomtypes.atp. Those are for ffnonbonded.itp. The atomtypes.atp file needs only the atom type and its mass as it is only used by pdb2gmx. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
Re: [gmx-users] Invalid atomtype format (Justin Lemkul)
Dear Justin I have shared the files for the users mailing list on the following link. https://www.dropbox.com/s/bfaq8z8iqojdm0r/Atom_type_error%20files.zip?dl=0 Thanks and Regards. Sadaf -- 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.
Re: [gmx-users] Invalid atomtype format
On 4/28/20 11:52 AM, Sadaf Rani wrote: Dear Gromacs users I am facing a problem between different versions of gromacs for gmx pdb2gmx. I have a protein-ligand system, I did all the necessary steps mentioned in gromacs manual for adding new residue to force field. When I run this in gromacs 2019 it gives me a warning as below:- Fatal error: Invalid atomtype format: '' But it still generates a gro file and topology. But When I am using gromacs 2020, I get the same message of invalid atomtype format as below:- Reading 78I-T.pdb... WARNING: all CONECT records are ignored Read '', 4083 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. WARNING: Chain identifier 'A' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. There are 2 chains and 0 blocks of water and 492 residues with 4083 atoms chain #res #atoms 1 'A' 489 3971 2 'A' 3112 All occupancies are one Opening force field file ./amber99sb-ildn.ff/atomtypes.atp --- Program: gmx pdb2gmx, version 2020-UNCHECKED Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98) Fatal error: *Invalid atomtype format: ''* I am unable to sort out this problem. I have added the atom types of my molecule as mentioned:- ;[ atomtypes ] ; name bond_type mass chargeptype sigma eps nh 14.01000 0.000 A 3.25000e-1 7.11280e-1 hn 1.00800 0.000 A 1.06908e-1 6.56888e-2 ca 12.01000 0.000 A 3.39967e-1 3.59824e-1 nb 14.01000 0.000 A 3.25000e-1 7.11280e-1 h5 1.00800 0.000 A 2.42146e-1 6.27600e-2 nc 14.01000 0.000 A 3.25000e-1 7.11280e-1 cd 12.01000 0.000 A 3.39967e-1 3.59824e-1 na 14.01000 0.000 A 3.25000e-1 7.11280e-1 c3 12.01000 0.000 A 3.39967e-1 4.57730e-1 h2 1.00800 0.000 A 2.29317e-1 6.56888e-2 os 16.0 0.000 A 3.1e-1 7.11280e-1 h1 1.00800 0.000 A 2.47135e-1 6.56888e-2 p5 30.97000 0.000 A 3.74177e-1 8.36800e-1 o 16.0 0.000 A 2.95992e-1 8.78640e-1 oh 16.0 0.000 A 3.06647e-1 8.80314e-1 ho 1.00800 0.000 A 0.0e+0 0.0e+0 h4 1.00800 0.000 A 2.51055e-1 6.27600e-2 c 12.01000 0.000 A 3.39967e-1 3.59824e-1 n 14.01000 0.000 A 3.25000e-1 7.11280e-1 ha 1.00800 0.000 A 2.59964e-1 6.27600e-2 Could you please help me to sort out this problem. Even when the format is incorrect does it mean that gromacs 2019 is generating a wrong topology? You should upload a complete test case (including all force field files and your PDB structure) somewhere so that we can take a look at it. This is a weird error to try to debug. Make sure you're only ever using a plain-text editor like VIM or Emacs to avoid inclusion of inappropriate characters. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
