Anna Marabotti wrote:
I hope this will be the last message on this subject...sorry to bother you,
but I'd need another hint about analysis.
All OK about the new reference file that I created following Justin's
suggestions.
The problem now is that my protein is a homodimeric protein, and when I do:
g_rmsf -f prot_boxdodfull_mol.xtc -s prot_boxdodfull_0ns_fix.gro -o
prot_boxdodfull_rmsf.xvg
the .xvg file comes with the analyses of both subunits superimposed. I tried
to avoid this first creating a .pdb file from the
prot_boxdodfull_0ns_fix.gro file:
editconf -f prot_boxdodfull_0ns_fix.gro -s prot_boxdodfull_0ns_fix.pdb
then adding the chain identifiers "A" and "B" to my .pdb file (I simply
edited it), and finally I used
g_rmsf -f prot_boxdodfull_mol.xtc -s prot_boxdodfull_0ns_fix_chain.pdb -o
prot_boxdodfull_rmsfchain.xvg
but still the .xvg file appears with the data about the two chains
superimposed.
I also tried to create an .ndx file, in which I created two groups (chA and
chB), but it seems to me that they are not suitable for my need.
Why not? This seems like the most obvious solution. If you analyze both chains
independently, isn't that what you're trying to achieve?
If you want to completely eliminate any reliance on chain identifiers or
overlapping numbers, either (1) eliminate all chain IDs or (2) make them all the
same, and then use genconf to renumber the whole coordinate file from 1.
-Justin
Do you have any hints about? FYI, I'm currently using Gromacs 4.5.4, and
therefore the residues of the proteins were not renumbered.
Thank you for your infinite patience...
Anna
-----Messaggio originale-----
Date: Mon, 11 Jul 2011 10:29:51 -0400
From: "Justin A. Lemkul" <[email protected]>
Subject: Re: [gmx-users] R: Re: g_mindist on rhombic dodecahedron
system
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Anna Marabotti wrote:
Dear Justin, dear all,
following your suggestion I used the command:
trjconv -f prot_boxdodfull.xtc -s prot_boxdodfull.tpr -pbc mol -ur compact
-o prot_boxdodfull_mol.xtc
to convert my simulations, and as you anticipated all went OK: now my
trajectories are without spikes, the protein is entirely in the rhombic
dodecahedric box and the minimum distance is never lower than 2.5 nm, so I
think that the simulations went properly.
Now I have another doubt. In order to analyze my data (e.g. with g_rmsf,
g_rms etc), which is the more correct reference file? Usually I use as
reference file the .tpr input file of the full MD trajectory. I used this
file also this time with the command:
g_rms -f prot_boxdodfull_mol.xtc -s prot_boxdodfull.tpr -o
prot_boxdodfull_rms.xvg
Apparently, there are no main irregular behaviours (the RMS value
oscillates
between 4.2 and 4.25 nm, so I think I can assume it is quite stable). The
absolute value of RMS is however very high with respect to the ones I used
to see (that are generally lower than 1 nm). I assume that the important
thing in this kind of analysis is the variation of the value, not the
value
itself; however, I would like to know if I use the correct reference file
or
if I have to create another reference file in which I "trjconv'ed" (how?)
also the reference structure. Could you please give me some suggestion
about
my question?
If you've manipulated the trajectory with trjconv, then you need a
corresponding
reference frame for position-dependent quantities. For RMSD, RMSF, etc I
usually do something like:
editconf -f start.tpr -o 0ns.gro
trjconv -s start.tpr -f 0ns.gro -pbc mol -ur compact -o 0ns_fix.gro
g_rms -s 0ns_fix.gro -f traj_fix.xtc
Other manipulations may be necessary if the protein is a dimer, etc.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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