[gmx-users] unknown cmap torsion between atoms

2012-05-25 Thread Steven Neumann
Dear Gmx Users, My system is made of 3 proteins. As I want to use distance restraints dynamics between atoms belonging to each of them I have to produce topoloy with one moleculetype. I used pdb2gmx -chainsep interactive (I used merge: yes). Then when I process to grompp the error: unknown cmap

Re: [gmx-users] unknown cmap torsion between atoms

2012-05-25 Thread Mark Abraham
On 25/05/2012 7:52 PM, Steven Neumann wrote: Dear Gmx Users, My system is made of 3 proteins. As I want to use distance restraints dynamics between atoms belonging to each of them I have to produce topoloy with one moleculetype. I used pdb2gmx -chainsep interactive (I used merge: yes).

Re: [gmx-users] unknown cmap torsion between atoms

2012-05-25 Thread Steven Neumann
On Fri, May 25, 2012 at 4:18 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 25/05/2012 7:52 PM, Steven Neumann wrote: Dear Gmx Users, My system is made of 3 proteins. As I want to use distance restraints dynamics between atoms belonging to each of them I have to produce topoloy with one

Re: [gmx-users] unknown cmap torsion between atoms

2012-05-25 Thread Justin A. Lemkul
On 5/25/12 5:52 AM, Steven Neumann wrote: Dear Gmx Users, My system is made of 3 proteins. As I want to use distance restraints dynamics between atoms belonging to each of them I have to produce topoloy with one moleculetype. I used pdb2gmx -chainsep interactive (I used merge: yes). Then

Re: [gmx-users] unknown cmap torsion between atoms

2012-05-25 Thread Steven Neumann
On Fri, May 25, 2012 at 2:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/25/12 5:52 AM, Steven Neumann wrote: Dear Gmx Users, My system is made of 3 proteins. As I want to use distance restraints dynamics between atoms belonging to each of them I have to produce topoloy with one

Re: [gmx-users] unknown cmap torsion between atoms

2012-05-25 Thread Justin A. Lemkul
On 5/25/12 5:04 PM, Steven Neumann wrote: On Fri, May 25, 2012 at 2:34 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/25/12 5:52 AM, Steven Neumann wrote: Dear Gmx Users, My system is made of 3 proteins. As I want to use distance restraints

[gmx-users] unknown cmap torsion between atoms

2011-10-31 Thread ram bio
Dear Gromacs users, I have built a protein embedded in popc bilayer and executed pdb2gmx using charmm27 ff on the system and the toplogy file was created without errors, but when wanted to minimise the system with grompp i am getting an error as : unknown cmap torsion between atoms 8377 8379 8381

Re: [gmx-users] unknown cmap torsion between atoms

2011-10-31 Thread ram bio
Hi Mark, Thanks for the response. I have built this system (protein in popc bilayer using charmm GUI) and submitted the total built system to pdb2gmx, is this the reason for having unknown CMAP torsion while executing grompp, by the way pdb2gmx doesnot show any error. Cant the charmm gui built

Re: [gmx-users] unknown cmap torsion between atoms

2011-10-31 Thread Mark Abraham
On 1/11/2011 2:16 PM, ram bio wrote: Hi Mark, Thanks for the response. I have built this system (protein in popc bilayer using charmm GUI) and submitted the total built system to pdb2gmx, is this the reason for having unknown CMAP torsion while executing grompp, by the way pdb2gmx doesnot