Re: [gmx-users] C-terminal amidation of peptide

2011-03-20 Thread Jianguo Li
2011 11:59:34 Subject: [gmx-users] C-terminal amidation of peptide Hello, I'm sorry if my questions are on the elementary level, as I am still learning how to use GROMACS. I would like perform an MD run on a peptide that has an amidated c-terminal. My understanding is that I can modify m

Re: [gmx-users] C-terminal amidation of peptide

2011-03-19 Thread Mark Abraham
On 20/03/11, anna Kalkbrenner wrote: > Hello, > > I'm sorry if my questions are on the elementary level, as I am still learning > how to use GROMACS.  I would like perform an MD run on a peptide that has an > amidated c-terminal.  My understanding is that I can modify my PDB structure > to

Re: [gmx-users] C-terminal amidation of peptide

2011-03-19 Thread Justin A. Lemkul
anna Kalkbrenner wrote: Hello, I'm sorry if my questions are on the elementary level, as I am still learning how to use GROMACS. I would like perform an MD run on a peptide that has an amidated c-terminal. My understanding is that I can modify my PDB structure to include the NH2 group. T

[gmx-users] C-terminal amidation of peptide

2011-03-19 Thread anna Kalkbrenner
Hello, I'm sorry if my questions are on the elementary level, as I am still learning how to use GROMACS. I would like perform an MD run on a peptide that has an amidated c-terminal. My understanding is that I can modify my PDB structure to include the NH2 group. Then, with pdb2gmx I use the "-t