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Mismatch between coordinate file and topology
- sri27
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7 years 5 months ago #6320
by sri27
Mismatch between coordinate file and topology was created by sri27
Dear All,
I have started to use MARTINI Forcefield to simulate proteins. I have taken the insulin pdb file from the pdb website (tried both 1ZNI and 4EWZ) and tried to use martinize.py to generate the topology. I got the following error
"number of coordinates in coordinate file (check.gro, 184) does not match topology (check.top, 232)"
As suggested in an earlier reply, I have tried removing everything other than the coordinate file and tried building the topology file, but the problem persists.
I have seen the files and found that the topology created has additional beads than those in the coordinate file (which is also clear from the error)
Can anyone suggest a way out ?
Thanks and Regards,
Sri
I have started to use MARTINI Forcefield to simulate proteins. I have taken the insulin pdb file from the pdb website (tried both 1ZNI and 4EWZ) and tried to use martinize.py to generate the topology. I got the following error
"number of coordinates in coordinate file (check.gro, 184) does not match topology (check.top, 232)"
As suggested in an earlier reply, I have tried removing everything other than the coordinate file and tried building the topology file, but the problem persists.
I have seen the files and found that the topology created has additional beads than those in the coordinate file (which is also clear from the error)
Can anyone suggest a way out ?
Thanks and Regards,
Sri
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- peterkroon
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7 years 4 months ago #6557
by peterkroon
Replied by peterkroon on topic Mismatch between coordinate file and topology
Hi Sri,
the error means that there's a different number of atoms in your .top file and .gro file. One of both does not correctly describe the system you want to simulate, and you'll need to correct it. Think of the amount of solvent or ions, or maybe you're still trying to use an atomistic .pdb with a coarse-grained topology, ...
Without more information, I can't be more specific.
the error means that there's a different number of atoms in your .top file and .gro file. One of both does not correctly describe the system you want to simulate, and you'll need to correct it. Think of the amount of solvent or ions, or maybe you're still trying to use an atomistic .pdb with a coarse-grained topology, ...
Without more information, I can't be more specific.
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