Error with ctp_map "WARNING: No Mapping instructions found for atom [...]"

[Michele Turelli]

Hi everyone,

I have already run the program a number of times without problems. Since a couple of days I keep running into the following (see attachment error.txt), repeated for all atoms and I am unable to produce the state.sql file.

ctp_map -t <topology_file>.tpr -c <whole_system>.pdb -s <mapping_file>.xml -f state.sql -v


the .tpr file has been obtained by running

gmx grompp -f <gromacs_file>.mdp -c <whole_system>.pdb -p <topology_file>.top -maxwarn 10

I attach the topology (top) file and the mapping file .xml, together with a transcript of the error.

If anybody can point out to me what I'm doing wrong I'd be incredibly thankful.

Regards.

[Denis Andrienko]

Hi Michele,

Have you recently updated the votca installation?

Can you attach the pdb file or the tpr file for me to confirm the issue?

Thanks,

Denis

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[Michele Turelli]

Thanks for the quick reply!

I did not update votca nor gromacs.
I can't figure out what I am doing differently.

I attach the file requested.

Thanks again,
Michele

[Denis Andrienko]

Hi Michele,

It seems that your residue number is zero in the pdb file:

HETATM    1  N1  1ME A   0     -39.000 -21.487  20.650                       N

While in the system.xml you should provide residue number to identify the atom.

ctp_map cannot find an 1:1ME:C7 atom, since it looks for the residue number one.

Please check that your pdb and your system.xml agree.

Best,
Denis

[Denis Andrienko]

In fact, you could use pdb2map next time you want to prepare system.xml. For your system

ctp_tools -e pdb2map -o pdb2map.xml 

would give conf.xml which has zero residue name.

I attach the input.

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