Re: [gmx-users] How to process D-amino acid peptide?

Thank you, David and Erik. The problem has been solved. -- View this message in context: http://gromacs.5086.x6.nabble.com/How-to-process-D-amino-acid-peptide-tp5013440p5013475.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please sea

Re: [gmx-users] How to process D-amino acid peptide?

pdb2gmx adds hydrogens if they are not present, which will be done in the L-form. If you already have hydrogens you should be able to maintain the residues in D-form. Cheers, Erik On 20 Dec 2013, at 09:56, David van der Spoel wrote: > On 2013-12-20 07:23, hummingbird wrote: >> I am doing a

Re: [gmx-users] How to process D-amino acid peptide?

On 2013-12-20 07:23, hummingbird wrote: I am doing a simulation of a system including a peptide made up of 36 D-amino acid residues. I am a new user and have no idea how to process D-amino acid. When I try pdb2gmx, all residues are changed to L-type in the output GRO file. Could anybody help? Tha

[gmx-users] How to process D-amino acid peptide?

I am doing a simulation of a system including a peptide made up of 36 D-amino acid residues. I am a new user and have no idea how to process D-amino acid. When I try pdb2gmx, all residues are changed to L-type in the output GRO file. Could anybody help? Thanks so much. -- View this message in co