Re: [gmx-users] naive question about the c-terminus

2010-05-10 Thread Justin A. Lemkul
010 11:00:06 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] naive question about the c-terminus > > > > abdullah ahmed wrote: > > I'm sorry I should have been more clear. Because the PDB file starts > > from resi

RE: [gmx-users] naive question about the c-terminus

2010-05-10 Thread abdullah ahmed
jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] naive question about the c-terminus > > > > abdullah ahmed wrote: > > I'm sorry I should have been more clear. Because the PDB file starts > > from residue number 23, the residue labelled 4

RE: [gmx-users] naive question about the c-terminus

2010-05-10 Thread abdullah ahmed
-0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] naive question about the c-terminus > > > > abdullah ahmed wrote: > > I'm sorry I should have been more clear. Because the PDB file starts > > from residue number 23, the resi

Re: [gmx-users] naive question about the c-terminus

2010-05-10 Thread Justin A. Lemkul
00 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] naive question about the c-terminus > > > > abdullah ahmed wrote: > > Hello everyone! > > > > I have a naive question and I have been trying to find a solution >

RE: [gmx-users] naive question about the c-terminus

2010-05-10 Thread abdullah ahmed
than one chains. Currectly I am working on one chain, but the original structure I was working on had 10 chains (from A -J). This is why it is labelled "B". > Date: Mon, 10 May 2010 10:29:18 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users]

Re: [gmx-users] naive question about the c-terminus

2010-05-10 Thread Justin A. Lemkul
abdullah ahmed wrote: Hello everyone! I have a naive question and I have been trying to find a solution myself, but I just don't understand what is wrong. When I run pdb2gmx with "-ter" on my molecule I get the following error message when I ask for a COOH to be made at the C terminus (I g

Re: [gmx-users] naive question about the c-terminus

2010-05-10 Thread XAvier Periole
On May 10, 2010, at 4:12 PM, abdullah ahmed wrote: Hello everyone! I have a naive question and I have been trying to find a solution myself, but I just don't understand what is wrong. When I run pdb2gmx with "-ter" on my molecule I get the following error message when I ask for a COOH to

[gmx-users] naive question about the c-terminus

2010-05-10 Thread abdullah ahmed
Hello everyone! I have a naive question and I have been trying to find a solution myself, but I just don't understand what is wrong. When I run pdb2gmx with "-ter" on my molecule I get the following error message when I ask for a COOH to be made at the C terminus (I get no error when I ask