Re: [gmx-users] make_ndx option

Hi Anirban, when you choose in make_ndx, you choose group 3 and (&) r 2 3 4 5 6...and so on... in make_ndx there is a legend that explain this passage well... Bye! 2009/7/9 Anirban Ghosh > Hi ALL, > > I want to create an index file using make_ndx which will contain only > C-alpha atoms of some r

Re: [gmx-users] Re: Problem with AMBER-GROMACS DNA database residue

Hi, Alan Thank you very much for your quick answer. You understand well my problem... I normally use amb2gmx for proteins, and, changing some residue names (ex. CYM-->CYS..), it works correctly... It's the first time that I work with DNA, and I have this problem... thank you for your help Rubben 2

[gmx-users] Problem with AMBER-GROMACS DNA database residue

Hi, gmx-users, I have a problem to "translate" nitrogen base residue names from AMBER to GROMACS. I have simulated with AMBER a DNA-protein complex, then i have changed in the prmtop file the standard nitrogen bases as DT--> DTHY, DG-->DGUA, DC-->DCYT, DA-->DADE, in order to "translate" the MDs fr