I want to create CHARMM topology for 100 ligands and using in GROMACS. I used Swissparam and created itp files for each ligand. I think, need merge all itp files in one for using in GROMACS. I opened some mol2 files in Chimera and created one mol2 files that include maximal near 15 ligands. If open more mol2 files, then Swissparam write error reason with atomname (not unique). I rename all atomname and made his unique, but Swissparam wrote error without some comments. How create this one charmm topology itp file or my steps is wrong? Maybe possible another solution merge all itp file ligands?
there are errors while generating mol2 format from Chimera...I face same problems while generating topology from swissparam using Chimera generated mol2 format.
I would rather suggest you to generate mol2 format from either avogadro or marvin sketch software.. these packages don't give errors in swissparam.
You do not need to merge .itp files of multiple ligands. You will certainly have duplicated atom types and possibly other parameters. One possible approach is to collate all of the atom types into one unified topology (e.g. "new_atomtypes.itp") and #include that in any .top file that will have a ligand, then have the ligand .itp files (without [atomtypes] defined in them) that can immediately be #included in any .top. Otherwise, just #include each ligand .itp file in the .top for whatever system to which it applies.
Thank you for your answers. I.e. I may #include in top file all 100 itp files together? But in Swissparam site give note: "It can happen that there is more that one small molecule in your system. Due to the fact that all [atomtypes] and [pairtypes] sections have to come before any [moleculetype] section, it is not possible to sequentially include two or more .itp files created by SwissParam. Instead, you will have to manually merge the contents of those itp files, such that the right order of sections is maintained."
- Badges
- Science topic