I am writing to seek assistance on a matter related to n2t file generation. I am using GROMACS and charmm36 force field in my work. I am covalently attaching a short polymer(poly-peptide) to a nanosheet with the carbonyl carbon of the polymer attached to the nitrogen of the nanosheet I obtained the parameter(itp file) for the polypeptide from CGENFF then added the corresponding atom types and charges from the itp to my n2t file the monomer of the poly-peptide is histidine and it’s itp file has various hydrogen atom type along with carbon types with different charges I have added them all in the n2t file in the same sequence as in the itp since most these atom types are attached to carbon when topology is created using x2top wrong type of carbon and consequently wrong charge is assigned to the atom of my structure. I want you to note the hydrogen types as well as the nitrogen type NG2R51 in the topology file at line 134 it is supposed to be a NG2S1 nitrogen type with a -0.555 charge. There are many other atoms whose atom type was supposed to be different. How can I obtain correct topology.I am attaching the itp file(plh.itp) along with the ss of topology and n2t file. Any guidance or pointers would be of immense help. Thank you for your time.
Aqsa Kamran
You have to go SWISSPARAM server to generate topology file for your complex. As my experience SWISSPARAM very suitable for gromacs.
Thank you very much for your suggestion, but as per my limited knowledge swissparam is appropriate for small molecule and would generate wrong atom types for atoms in the nanosheet.
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