VOTCA xtp_map "atom entry is not well formatted"
Xixian
Hello,
I’m now using VOTCA XTP for calculating charge mobility. I’m stuck on the first mapping step. When I run xtp_map, it reminds me that “Atom entry 1:BDF:C1 is not well formatted” as the attached screenshot shows.
To make my issue clearer, I’m using VOTCA version 2024.2 and GROMACS 2019.6. Additionally, I have the screenshot of part of my pdb file,.top file and and .xml file attached.
I tried one molecule in the simulation box and tested the mapping files. This molecule can be further divided into 14 segments. In this one molecule, I have three types of residues and residue number spanning from 1 to 14 (12 of them have the same residue name but different residue number). I also have atom number and residue name (3 different names) defined for the whole molecule. Correspondingly, I have .top file where the atom number, atom name, residue name and residue number that are exactly same as those in .pdb file. Later on together with mdp file, I have my tpr file and xtc file prepared.
For xml file, I composed that manually. I tried the residue number both start from 0 and 1 (since I see some other posts whose atom index starts from 1 in pdb but xml with 0), neither of them works and both gives me the “not well formatted” error. I also tried the <qmatoms> index from either 0 or 1. I guess I might misunderstand anything here. I don’t have any ideas now to address0 this issue. I’m wondering if anyone in this community could help with this issue. Thanks.
