Hi Michael,
The error message indicates that one of your residues in your PDB has an incorrect number of atoms. This is one of the checks that the script does on the molecules while processing it. Basically, the script does a substitution on each atom in the residue and if it finds the incorrect number of atoms then it stops.
Residues are split in the PDB by the residue number field of the PDB and identified by the residue sequence field and TER cards. The script only processes C36 lipids, water, and some ions. All other residues are ignored.
So, first check if the residues to be converted (lipids, water, ions) match the template of substitution file (charmmlipid2amber.csv). If there is no problem there, then it is probably a problem with residue sequence or TER. The script assumes that the normal PDB residue sequence and TER cards are used.
Best,
Ben
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Received on Wed Apr 08 2015 - 20:30:02 PDT
