[gmx-users] Invalid atomtype format
Sadaf Rani
sadafrani6 at gmail.com
Tue Apr 28 17:52:52 CEST 2020
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
More information about the gromacs.org_gmx-users
mailing list