Re: [gmx-users] gramicidin A

pragya chohan wrote: I had already read the refered pages . Great. I had made changes in the charge and improper dihedrals. Since you don't need to do this, it's best not to do this. But pdb2gmx doesnt seem to recognise those amino acids still. So your .rtp is broken somehow. Probably

RE: [gmx-users] gramicidin A

> Date: Sat, 3 Nov 2007 19:23:32 +1100> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] gramicidin A>> pragya chohan wrote:>> hi>> I was trying to run pdb2gmx command for gramicidin and noticed

Re: [gmx-users] gramicidin A

pragya chohan wrote: hi I was trying to run pdb2gmx command for gramicidin and noticed it has some D-amino acids. D-amino acids are enantiomers of L-amino acids. Thus they're topologically identical. So you can use the same topology for them, unless your force field has an interaction that v

[gmx-users] gramicidin A

hi I was trying to run pdb2gmx command for gramicidin and noticed it has some D-amino acids. Reading the earlier mail wjich states that: It's not too difficult to add a new residue to the topology database. Have a look in the file ff.rtp, where is the force field you are using. You can proba

Re: [gmx-users] Gramicidin A

Hello everyone, I am interested in simulating gramicidin A channel in DPPC membrane. I noticed there were few papers already published on this particularly Biophysics Journal Vol. 82 June 2002, by de Groot, Tieleman, Pohl and Grubmuller. Does anyone has the structure along with the topology f

[gmx-users] Gramicidin A

Hello everyone,I am interested in simulating gramicidin A channel in DPPC membrane.I noticed there were few papers already published on this particularlyBiophysics Journal Vol. 82 June 2002, by de Groot, Tieleman, Pohl and Grubmuller. Does anyone has the structure along with the topology files so t