[gmx-users] complex topology nr error

Sana Saeed bioinformatic.lady at yahoo.com
Sun Feb 28 11:48:09 CET 2016

[history: i am working on ligand protein complex to find out free binding energy. i amde complex topology, and you suggested that i should put my distance restraints directive after molcules directive, when i did so it gave me error about atom 2023 out of range (2023 is my ligand atom, but in topology it is atom number 3. then i changed the directives places like mentioned following:1.   #include ff2.    [moleculetype]      protein         ligand
3.   protein topogy contents4.   #include "ligand.itp5.   [distance restraints6.    [angle restraints]7.    [dihedral restraints]8.    Position restraint complex9. water topology and restraints10. ions topology11. [system]12. [molecules]i got this errorAtoms in the .top are not numbered consecutively from 1 (rather, atomnr = 1, while at->nr = 2121)
: this is because in the topology file 2121 is SOL (water molecule) what should i do now.
 Sana Saeed Khan,Teaching-Research AssistantChemoinformatics LabGraduate Student, MS bioinfoDepartment of BioinformaticsSoongsil University, Seoul, South Korea.

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