[gmx-users] Re: hydrophobic contacts

Hi all thanks for your valuable suggestions. But still i'm not clear. I have tried using the .tpr file with make_ndx but the index group is displayed is similar to that of the one with .gro file. I have manually identified the residues and when i ran the g_mindist with the ligand 0f 18 atoms

Re: [gmx-users] Re: hydrophobic contacts

On 11/14/12 2:27 AM, Raj wrote: Hi all, can some one tel me how can i prepare a index file specifying the hydrophobic atoms along for measuring the hydrophobic contacts in the systems alone. There is no straightforward way to do this, as far as I know. I generally construct such groups

Re: [gmx-users] Re: hydrophobic contacts

Hi, if you don't want to be very accurate, you can select basing on the residue name since LEU, ILE, VAL...etc, are universally considered hydrophobic 2012/11/14 Justin Lemkul jalem...@vt.edu On 11/14/12 2:27 AM, Raj wrote: Hi all, can some one tel me how can i prepare a index file

[gmx-users] Re: hydrophobic contacts

Hi all, can some one tel me how can i prepare a index file specifying the hydrophobic atoms along for measuring the hydrophobic contacts in the systems alone. -- View this message in context: http://gromacs.5086.n6.nabble.com/hydrophobic-contacts-tp4998153p5002931.html Sent from the GROMACS