Re: [gmx-users] Problem with amidation in pdb2gmx

Yeah. I select none for the terminal residues. Gromacs was compiled by myself. I have used this version in production runs for the last 5 months. Cheers Mitch Justin A. Lemkul wrote: Sorry, clicked 'send' too soon. How was this version of Gromacs compiled? I remember submitting a bugzilla

Re: [gmx-users] Problem with amidation in pdb2gmx

Sorry, clicked 'send' too soon. How was this version of Gromacs compiled? I remember submitting a bugzilla not too long ago about a similar problem, and it ended up being that the Ubuntu package was broken. Re-compiling from source fixed the problem. The -ter response was a knee-jerk reaction,

Re: [gmx-users] Problem with amidation in pdb2gmx

Quoting [EMAIL PROTECTED]: > Hello all, > > I have a protein with missing N- and C- terminus residues. I am > simulating a complex. To avoid in-silico charge interactions at the > wrong places due to the missing residues I have performed acetylation > and amidation. > > > When running pdb2gmx (GMX

Re: [gmx-users] Problem with amidation in pdb2gmx

Quoting [EMAIL PROTECTED]: > Hello all, > > I have a protein with missing N- and C- terminus residues. I am > simulating a complex. To avoid in-silico charge interactions at the > wrong places due to the missing residues I have performed acetylation > and amidation. > > > When running pdb2gmx (GMX

[gmx-users] Problem with amidation in pdb2gmx

Hello all, I have a protein with missing N- and C- terminus residues. I am simulating a complex. To avoid in-silico charge interactions at the wrong places due to the missing residues I have performed acetylation and amidation. When running pdb2gmx (GMX331) I experience a problem - pdb