Re: [gmx-users] GROMACS AMBER DNA TERMINUS

I guess you misunderstood that. What you have there, is the terminal hydrogen, which is an hydroxyl one and therefore fully ok. You should search for an atom at the nucleobase, which has atom type 25. This usually has to be changed. Strange error, though :) I think its somewhere around N1 for g

Re: [gmx-users] GROMACS AMBER DNA TERMINUS

___ Erik Marklund, PhD student Laborarory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED]

[gmx-users] GROMACS AMBER DNA TERMINUS

Dear All, I am using Gromacs 3.1.1 with the AMBER port. After following the instructions on the ffamber web-page, pdb2gmx works fine. But according to point 6: "... However, for nucleic acids this also often causes pdb2gmx to replace an H atom in the first residue of all nucleic acid chains