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' 3 112 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 charge ptype 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 16.00000 0.000 A 3.00001e-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 16.00000 0.000 A 2.95992e-1 8.78640e-1 oh 16.00000 0.000 A 3.06647e-1 8.80314e-1 ho 1.00800 0.000 A 0.00000e+0 0.00000e+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? Thanks in advance. 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.