Gen_syst.py
Gen_syst.py is a program to generate a syst1 file for ComQum
made by Justin Bergmann 2020
The program i located in /home/justin/snic2019-35-66/Justin/programs/scripts/gen\_syst1.py
with copies in
/home/ulf/Bio/Comqum
To use the program, you need to load the modules:
module load GCCcore/8.3.0
module load Python/3.7.4
Needed files
comqum.pdb - the pdb file
qm.txt - a file contain a list of atoms you want to have in your syst1.
Format of qm.txt
pdb line with ATOM or HETATM as (only atom name, chain and residue number is used):
ATOM 8594 O HOH
A2151 25.823 15.680
18.506 1.00 38.74
A O
or a complete residue:
RESI A 501
or an atom by its name residue and chain:
ANAM NH1 96 A
only heavy atoms in the syst1 are needed but H atoms do not harm.
truncation atoms are not included in the qm.txt file - they are added automatically.
Run the program
If the pdb file is not already protonated it is possible to protonate
C,N,O at standard positions (this is an initial guess and MUST be
modified by hand later on - 90% of work is done)
gen_syst1.py qm.tex comqum.pdb P
All files are necessary but the names of the qm.tex file is flexible
Writes out a syst1 file and a comqum.pdb file
Run without protonation:
gen_syst1.py qm.tex pdb
Adds existing H atoms to the syst1 file but does not change the comqum.pdb file Writes out the syst1 file
Default names:
gen_syst1.py comqum.pdb
qm.txt and comqum.pdb are default names
Adds existing H atoms to the syst1 file but does not change the comqum.pdb file Writes out syst1 file
it always writes out a restart\_anam file whit can use as a new qm.txt file with all atom names