[gmx-users] N-terminal PGLU and C-term amidation

Hello, I am new to gromacs. I am applying the pdb2gmx tool to a peptide that has an N-term pyroglutamate and a C-term amidation. The OPLS forcefield has an entry for PGLU. I used the -ter flag of pdb2gmx to define protonation states of the termini. While this works fine for the C-term (ch

[gmx-users] N-terminal and C-terminal capping in MARTINI

Does anyone know if the current MARTINI version have parameters for N-terminal and C-terminal caps other than NH3+ and COO- ? Thank you -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org h

Re: [gmx-users] n terminal

shahrbanoo karbalaee wrote: thank you justin in papers net charge of peptide is calculated +1,with amidated in terminal. that I defined with flag -ter in pdbf2gmx .and when I add tfein system I see in pdb files lys is changed LYSH. OK, so your peptide has a +1 charge

[gmx-users] n terminal

thank you justin in papers net charge of peptide is calculated +1,with amidated in terminal. that I defined with flag -ter in pdbf2gmx .and when I add tfein system I see in pdb files lys is changed LYSH. best -- sh-karbalaee ___

Re: [gmx-users] N-terminal and C-terminal modifications

List User wrote: What is the best approach to handle N and C-terminal modifications (e.g. formylation, chemical modification)? Is it better to define custom residue types or to adjust the termini database? Thanks in advance for your advice. I would suggest custom residue types and/or termini,

[gmx-users] N-terminal and C-terminal modifications

What is the best approach to handle N and C-terminal modifications (e.g. formylation, chemical modification)? Is it better to define custom residue types or to adjust the termini database? Thanks in advance for your advice. ___ gmx-users mailing list