[gmx-users] error in pdb2gmx

Sadaf Rani sadafrani6 at gmail.com
Sun Apr 19 18:48:32 CEST 2020


Dear Gromacs users
I have tried to sort out this problem with gromacs 2020 and 2019 versions.
I gromacs 2019, It gives:-

All occupancies are one
Opening force field file ./amber99sb-ildn.ff/atomtypes.atp
Atomtype 106
Invalid format:
However, It generates a topology file.
In gromacs 2020, it gives:-

Program:     gmx pdb2gmx, version 2020-UNCHECKED
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98)

Fatal error:
Invalid atomtype format: ''

I have modified my atomtypes.atp file as below:-

;[ atomtypes ]
; name  mass
nh 14.01
dnh 14.01
hn 1.008
dhn 1.008
ca 12.01
dca 12.01
nb 14.01
dnb 14.01
h5 1.008
dh5 1.008
nc 14.01
dnc 14.01
cd 12.01
dcd 12.01
na 14.01
dna 14.01
c3 12.01
dc3 12.01
h2 1.008
dh2 1.008
os 16
dos 16
h1 1.008
dh1 1.008
p5 30.97
dp5 30.97
o 16
do 16
oh 16
doh 16
ho 1.008
dho 1.008
h4 1.008
dh4 1.008
c 12.01
dc 12.01
n 14.01
dn 14.01
ha 1.008
dha 1.008
Atomtype 106 is ha, I cant find any thing wrong with it. Could you please
help me to fix this error?

Thanks.
Sadaf


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