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Parametrization using 2.2P force field
- James Starlight
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Topic Author
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8 years 1 month ago #5440
by James Starlight
Parametrization using 2.2P force field was created by James Starlight
Dear MARTINI users!
I would like to perform CG simulation of water-soluble protein with the explicitly treatment of the electrostatic effect of solvent because that forces are important within my particular case.
I have faced with the problem of the usage of Martini 2.2p force field
while executing
python martinize.py -f 5AXS_proc_fix.pdb -x test.pdb -o topol_cg.top
-dssp /projects/clouddyn/Software/dssp -p backbone -ff martini22p
I obtained below warnings from the python script
WARNING Bead names of charges in sidechains differ between
.top/.itp and .pdb.
WARNING Using names in topology, as Gromacs does, gives the correct result.
and then grompp gave me error regarding mismatched atoms in my pdb and itp
Excluding 1 bonded neighbours molecule type 'Protein_A'
Warning: atom name 5 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 6 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 18 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 21 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 22 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 27 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 28 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 33 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 36 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 37 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 42 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 43 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 48 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 53 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 58 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 59 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 62 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 65 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 66 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 71 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
(more than 20 non-matching atom names)
WARNING 1 : 58 non-matching atom names atom names from topol_cg.top will be used atom names from test-CG.gro will be ignored At same time I have no such problem using older martini2.1p force field or not polarizable version 2.2 for the parametrization of the same systems How I could solve the issue? Thanks in advance! James[file topol_cg.top, line 14]:
58 non-matching atom names
atom names from topol_cg.top will be used
atom names from test-CG.gro will be ignored
At same time I have no such problem using older martini2.1p force field or not polarizable version 2.2 for the parametrization of the same systems
How I could solve the issue?
Thanks in advance!
James
I would like to perform CG simulation of water-soluble protein with the explicitly treatment of the electrostatic effect of solvent because that forces are important within my particular case.
I have faced with the problem of the usage of Martini 2.2p force field
while executing
python martinize.py -f 5AXS_proc_fix.pdb -x test.pdb -o topol_cg.top
-dssp /projects/clouddyn/Software/dssp -p backbone -ff martini22p
I obtained below warnings from the python script
WARNING Bead names of charges in sidechains differ between
.top/.itp and .pdb.
WARNING Using names in topology, as Gromacs does, gives the correct result.
and then grompp gave me error regarding mismatched atoms in my pdb and itp
Excluding 1 bonded neighbours molecule type 'Protein_A'
Warning: atom name 5 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 6 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 18 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 21 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 22 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 27 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 28 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 33 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 36 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 37 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 42 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 43 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 48 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 53 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 58 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 59 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 62 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 65 in topol_cg.top and test-CG.gro does not match (SCP - SCD)
Warning: atom name 66 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
Warning: atom name 71 in topol_cg.top and test-CG.gro does not match (SCN - SCD)
(more than 20 non-matching atom names)
WARNING 1 : 58 non-matching atom names atom names from topol_cg.top will be used atom names from test-CG.gro will be ignored At same time I have no such problem using older martini2.1p force field or not polarizable version 2.2 for the parametrization of the same systems How I could solve the issue? Thanks in advance! James[file topol_cg.top, line 14]:
58 non-matching atom names
atom names from topol_cg.top will be used
atom names from test-CG.gro will be ignored
At same time I have no such problem using older martini2.1p force field or not polarizable version 2.2 for the parametrization of the same systems
How I could solve the issue?
Thanks in advance!
James
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- peterkroon
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8 years 2 weeks ago #5459
by peterkroon
Replied by peterkroon on topic Parametrization using 2.2P force field
Hi
IIRC the "polarization" beads were renamed from sidechain positive/negative (SCN/SCP) to sidechain dummy (SCD). But apparently this hasn't been implemented correctly in Martinize.
I don't think you'll have any problems if you ignore Grompp's warning, but YMMV. If you're unsure, try reproducing some of the published results.
Good luck,
Peter
IIRC the "polarization" beads were renamed from sidechain positive/negative (SCN/SCP) to sidechain dummy (SCD). But apparently this hasn't been implemented correctly in Martinize.
I don't think you'll have any problems if you ignore Grompp's warning, but YMMV. If you're unsure, try reproducing some of the published results.
Good luck,
Peter
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