Re: [gmx-users] rmsf question

2010-03-16 Thread Andrei Neamtu
Dear Mark and Tjerk, Thank you for your comments. If I correctly uderstand the RMSF computed on C-alpha in PDB NMR structure, is a measure of the uncertanty in resolving the structure. Compared to this the RMSF of C-alpha computed from a MD trajectory reflects the geometric fluctuations of the

Re: [gmx-users] rmsf question

2010-03-16 Thread XAvier Periole
On Mar 16, 2010, at 9:43 AM, Andrei Neamtu wrote: Dear Mark and Tjerk, Thank you for your comments. If I correctly uderstand the RMSF computed on C-alpha in PDB NMR structure, is a measure of the uncertanty in resolving the structure. Well, the uncertainty of the NMR experiment would be

Re: [gmx-users] rmsf question

2010-03-16 Thread Mark Abraham
On 16/03/2010 8:17 PM, XAvier Periole wrote: On Mar 16, 2010, at 9:43 AM, Andrei Neamtu wrote: Dear Mark and Tjerk, Thank you for your comments. If I correctly uderstand the RMSF computed on C-alpha in PDB NMR structure, is a measure of the uncertanty in resolving the structure. Well, the

Re: [gmx-users] rmsf question

2010-03-16 Thread XAvier Periole
On Mar 16, 2010, at 10:24 AM, Mark Abraham wrote: On 16/03/2010 8:17 PM, XAvier Periole wrote: On Mar 16, 2010, at 9:43 AM, Andrei Neamtu wrote: Dear Mark and Tjerk, Thank you for your comments. If I correctly uderstand the RMSF computed on C-alpha in PDB NMR structure, is a measure of

Re: [gmx-users] rmsf question

2010-03-16 Thread Tsjerk Wassenaar
Hi Andrei, If I correctly uderstand the RMSF computed on C-alpha in PDB NMR structure, is a measure of the uncertanty in resolving the structure. No, that's not what I said. You're saying that there's one structure (the structure), but there is uncertainty in resolving it. That's not the case.

Re: [gmx-users] rmsf question

2010-03-15 Thread Andrei Neamtu
Dear Mark, Thank you very much for your response. What I meant was to obtain a RMSF plot form PDB mediated on each residue and to compare with a RMSF plot mediated on each residue obtained from a MD trajectory. I do not compare a frame from PDB with a frame from MD trajectory. So, in the PDB

Re: [gmx-users] rmsf question

2010-03-15 Thread Tsjerk Wassenaar
Hi Andrei, You can do it this way. But do mind that the ensemble from NMR is not meant to reflect the Boltzmann distribution. Rather it is meant to provide a number of plausible solutions given the (positive) restraints from the experiments and the force field used for the refinement. This means

Re: [gmx-users] rmsf question

2010-03-15 Thread Mark Abraham
On 15/03/2010 6:45 PM, Andrei Neamtu wrote: Dear Mark, Thank you very much for your response. What I meant was to obtain a RMSF plot form PDB mediated on each residue and to compare with a RMSF plot mediated on each residue obtained from a MD trajectory. I do not compare a frame from PDB with

[gmx-users] rmsf question

2010-03-14 Thread Andrei Neamtu
Hi, is there a rapid way to compute RMSF on an NMR ensemble from a PDB file? g_rmsf needs a .tpr file. This is OK with the MD trajectories but if I want to compare MD ensemble one with the NMR RMSF ensemble fluctuations from the original PDB this is not possible. Thanks, Andrei -- gmx-users

Re: [gmx-users] rmsf question

2010-03-14 Thread Mark Abraham
On 14/03/2010 7:47 PM, Andrei Neamtu wrote: Hi, is there a rapid way to compute RMSF on an NMR ensemble from a PDB file? Yes, but that's not your problem, it seems :-) g_rmsf needs a .tpr file. Not true. Inspect the lines in g_rmsf -h describing the file types suitable for -f and -s.