Hi,
if you were able to obtain a simulation it means you had a valid .top file!
In any case, gromacs recognises disulfide basing on the distance beween the
SG atoms.
In addition, the two chains are supposed to be in the same molecule.
So, my advice is, remove all the TER from pdb (but the last
Thanks Francesco.
But my problem is exactly opposite. I do have a .top file containing
both chain linked by disulfide bridge. I ran the simulation. Now I
have extracted .xtc file for each chain separately and I want the
corresponding, separate .top file for each chain. when I separate the
pdb and
Could you simply edit the file and removing the atom from [atoms] section ?
grompp wil complain regarding the line containing interactions. But also
these
few lines can be removed. Otherwise, vmd has the TopoTools that write the
.top
topology of the loaded pdb. Unfortunately, this topologyes are
I did it. Simply I changed the name of Cys which forms interchain
dsiulfide bond to CYS2 in the separated pdb file and I used G43a1
forcefeild to run pdb2gmx. This gives a topology with same number of
atom which is present in .xtc file. CYS2 is present .rtp file of G43a1
forcefeild probably to
If it works then you are right :)
2013/3/19 shahid nayeem msnay...@gmail.com
I did it. Simply I changed the name of Cys which forms interchain
dsiulfide bond to CYS2 in the separated pdb file and I used G43a1
forcefeild to run pdb2gmx. This gives a topology with same number of
atom which is
On 3/18/13 12:35 PM, shahid nayeem wrote:
Hi
Is it possible to write .top file from .xtc and .tpr using index.ndx
so that .top is available for tailormade components of simulated
protein.
All topology information is in the .tpr, but not in .top format. You may be
able to post-process the
Hi
To be more clear I have .xtc file for a disulfide linked complex of
two chains. From this trajectory I can extract .xtc file for
individual chains. But when I generate .top file from individual chain
pdb I get one atom extra in .top file i.e. protonated SG of Cys which
I dont need in order to
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