Hi everyone!
I have a 20 ns simulation (2fs timestep but coordinates saved every 0.2 ps)
and I was able to calculate the mean-square-displacement of the oxygen atoms of
my water solvent. The entire MSD plot looks very linear to me. I need to fit
this set of MSD data to obtain the diffusion co
Thank you Mark and Francesco,
I have repaired the trajectory and only lost 2 frames (40 ps total lost of 500
ns).
I used to automate a gmxcheck of each .xtc segment generated with mdrun
-noappend and
rerun segments that were corrupted ... I may go back to that usage in the
future.
For comple
@ram...
why dont u post what u did along with the part of the structure/file
attached ...
and what is the error and what u did to rectify...
and as per as i know, if u are working with DNA system along with CHARMM
forcefield, u should be careful with the atom types ...
since u haven't mentioned.
On 6/9/12 10:30 AM, James Starlight wrote:
Justin,
I have also question about inclussion of the part of the topology file wich was
done by the external server ( e.g by ATB) in the topology of my molecule.
E.g I'm working with GFP wich include non-standart chromophore group wich is
covalent bo
Justin,
I have also question about inclussion of the part of the topology file wich
was done by the external server ( e.g by ATB) in the topology of my
molecule.
E.g I'm working with GFP wich include non-standart chromophore group wich
is covalent bonded to the all protein. So I've extracted chro
On 9/06/2012 11:08 PM, ramaraju801 wrote:
as i said my system is an protein-DNA complex and the error popped up only
for atoms in DNA residues.
That's about 1% of the detail you'll need to provide in order for it to
be worth any more of anybody's time helping you :-) See
http://www.gromacs.or
as i said my system is an protein-DNA complex and the error popped up only
for atoms in DNA residues.
-ram
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On 6/9/12 8:53 AM, ramaraju801 wrote:
@ Mark,
i added -ter to pdb2gmx command and produced the topology file but still the
energy minimization step in vacuum is producing the same error
@justin
am presently running the simulation step i.e energy minimization of
structure in vacuum.
when produ
@ Mark,
i added -ter to pdb2gmx command and produced the topology file but still the
energy minimization step in vacuum is producing the same error
@justin
am presently running the simulation step i.e energy minimization of
structure in vacuum.
when producing the topology file ,it gave errors say
On 6/9/12 8:31 AM, ramaraju801 wrote:
correction i added O2 atom to atomtypes.atp file
The atomtypes.atp file is only used by pdb2gmx to make sure it can write certain
atom types. If you're introducing a new atom type, its parameters need to go in
ffnonbonded.itp, and if it is involved in
On 6/9/12 8:30 AM, ramaraju801 wrote:
yes, when creating the topology file i added atom O2 to the .rtp file when it
said atom O2 is missing in atomstype
It would be useful to show us what you're doing and explain what you're
attempting. But the answer remains the same - you cannot use atom
On 9/06/2012 10:30 PM, ramaraju801 wrote:
yes, when creating the topology file i added atom O2 to the .rtp file when it
said atom O2 is missing in atomstype
Adding O2 to any file is an effective solution. You need to fix your
termini properly, by using pdb2gmx -ter or the contents of your
co
correction i added O2 atom to atomtypes.atp file
regards,
ram
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yes, when creating the topology file i added atom O2 to the .rtp file when it
said atom O2 is missing in atomstype
regards,
ram
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On 6/9/12 7:24 AM, ramaraju801 wrote:
hi
am working on a DNA-protein complex, during the energy minimization step its
giving the following error,
"Fatal error:
Atomtype O2 not found"
am using charmm27 force field and used the command "grompp -f minim.mdp -c
protein.gro -p protein.top -o prote
hi
am working on a DNA-protein complex, during the energy minimization step its
giving the following error,
"Fatal error:
Atomtype O2 not found"
am using charmm27 force field and used the command "grompp -f minim.mdp -c
protein.gro -p protein.top -o protein-EM-vacuum.tpr "
regards,
ram
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