RE: [gmx-users] Adding two peptides in a water box

Subject: Re: [gmx-users] Adding two peptides in a water box From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Hi Everybory, I would like to simulate the interaction between two separated peptides in a water box. Every peptide needs to be N-and C-terminated. I have tried different

[gmx-users] Adding two peptides in a water box

Hi Everybory, I would like to simulate the interaction between two separated peptides in a water box. Every peptide needs to be N-and C-terminated. I have tried different alternatives in order to create the corresponding GROMACS files to start my simulation. I have used the GROMACS porograms

Re: [gmx-users] Adding two peptides in a water box

Hi Everybory, I would like to simulate the interaction between two separated peptides in a water box. Every peptide needs to be N-and C-terminated. I have tried different alternatives in order to create the corresponding GROMACS files to start my simulation. I have used the GROMACS porograms

RE: [gmx-users] Adding two peptides in a water box

_ Capture your memories in an online journal! http://www.reallivemoms.com?ocid=TXT_TAGHMloc=us___ gmx-users mailing listgmx-users@gromacs.org

RE: [gmx-users] Adding two peptides in a water box

Hi Luciano, use the -label option to separately label the gro files (e.g A for the first peptide and B for the 2nd), before you cat them with an editor. pdb2gmx should now recognise them as separate molecules. Rgds John Date: Sat, 8 Sep 2007 15:43:33 +0200 Subject: Re: [gmx-users] Adding two

Re: [gmx-users] Adding two peptides in a water box

Hi, why do you run pdb2gmx for the dimer? run it for the monomer, and then just put a Protein 2 instead of a Protein 1 (or however you name it) at the end of your topol.top file (just as is done for the water molecules, ions, etc). Lars Clarifying, if the two peptides are identical, then