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Error in martinize.py (Missing Atoms)
- miryawar
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10 years 6 months ago #2848
by miryawar
Error in martinize.py (Missing Atoms) was created by miryawar
Dear All
i am new to MD simulations.i want to generate CG structure to be used in the Gromacs.
i use the following command
python martinize.py -f protein.pdb -o protein.top -x cgprotein.pdb -dssp /home/yawar/simulations/martini/files/05-scripts/dsspcmbi
And i get the following error
INFO MARTINIZE, script version 2.3
INFO If you use this script please cite:
INFO de Jong et al., J. Chem. Theory Comput., 2013, DOI:10.1021/ct300646g
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO The martini21 forcefield will be used.
INFO Local elastic bonds will be used for extended regions.
INFO Read input structure from file.
INFO Input structure is a PDB file.
INFO Found 1 chains:
INFO 1: A (Protein), 4184 atoms in 532 residues.
INFO Total size of the system: 532 residues.
==== Secondary Structure Definition by the program DSSP, updated CMBI version by ElmK / April 1,2000 ====
INFO Writing coarse grained structure.
ERROR Too many atoms missing from residue TYR 305(ch:A):
ERROR
ERROR Too many atoms missing from residue LYS 306(ch:A):
ERROR
ERROR Too many atoms missing from residue LYS 343(ch:A):
ERROR
ERROR Too many atoms missing from residue ARG 442(ch:A):
ERROR
ERROR Too many atoms missing from residue ARG 476(ch:A):
ERROR
ERROR Too many atoms missing from residue ARG 517(ch:A):
ERROR
ERROR Too many atoms missing from residue ARG 587(ch:A):
ERROR
ERROR Unable to generate coarse grained structure due to missing atoms.
please please help regarding this issue>>
thanks in advance
i am new to MD simulations.i want to generate CG structure to be used in the Gromacs.
i use the following command
python martinize.py -f protein.pdb -o protein.top -x cgprotein.pdb -dssp /home/yawar/simulations/martini/files/05-scripts/dsspcmbi
And i get the following error
INFO MARTINIZE, script version 2.3
INFO If you use this script please cite:
INFO de Jong et al., J. Chem. Theory Comput., 2013, DOI:10.1021/ct300646g
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO The martini21 forcefield will be used.
INFO Local elastic bonds will be used for extended regions.
INFO Read input structure from file.
INFO Input structure is a PDB file.
INFO Found 1 chains:
INFO 1: A (Protein), 4184 atoms in 532 residues.
INFO Total size of the system: 532 residues.
==== Secondary Structure Definition by the program DSSP, updated CMBI version by ElmK / April 1,2000 ====
INFO Writing coarse grained structure.
ERROR Too many atoms missing from residue TYR 305(ch:A):
ERROR
ERROR Too many atoms missing from residue LYS 306(ch:A):
ERROR
ERROR Too many atoms missing from residue LYS 343(ch:A):
ERROR
ERROR Too many atoms missing from residue ARG 442(ch:A):
ERROR
ERROR Too many atoms missing from residue ARG 476(ch:A):
ERROR
ERROR Too many atoms missing from residue ARG 517(ch:A):
ERROR
ERROR Too many atoms missing from residue ARG 587(ch:A):
ERROR
ERROR Unable to generate coarse grained structure due to missing atoms.
please please help regarding this issue>>
thanks in advance
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- Clement
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10 years 6 months ago #2849
by Clement
Replied by Clement on topic Error in martinize.py (Missing Atoms)
Welcome on The Forum Miryawar.
The problem comes from the fact the residues mentioned at the bottom of the error message you receive are not complete in the PDB structure you're using. It's most of the time possible to complete them with pymol or so, by mutating the broken residues into full ones.
Rerun the martinize command line after that, and everything should be fine.
The problem comes from the fact the residues mentioned at the bottom of the error message you receive are not complete in the PDB structure you're using. It's most of the time possible to complete them with pymol or so, by mutating the broken residues into full ones.
Rerun the martinize command line after that, and everything should be fine.
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