parichita parichita wrote:
Thaks for your suggesion...
I want to use Gromacs for MD on my disaccharides in explicit water box.Now, the
problem I encounter is that the pdb2gmx produces the topologies where hydrogens
sitting on carbons are condensed on carbon atoms they sit on. I need them
Thaks for your suggesion...
I want to use Gromacs for MD on my disaccharides in explicit water box.Now, the
problem I encounter is that the pdb2gmx produces the topologies where hydrogens
sitting on carbons are condensed on carbon atoms they sit on. I need them
explicitly
since I would
parichita parichita wrote:
Hi again.
Thank you for your help
I found my MANA in the ffG53a5.rtp and i can prepare
the .gro and .top file from pdb2gmx.
Now , i am facing another problem after solvation of
my solute when i run the minimization the 1-6 linkage
was broken ..
please
Parichita,
My guess is you only thought to have 1-6 linkage, because the atoms
seemed so nicely involved in the .pdb file. But you'll have to define
a bond explicitly or it won't be there to break in the first place. I
think you need to read up on topologies, force fields and general
background
Hi,
I have facing some problem when converting .pdb file to .gro and .top .
I have a .pdb of alpha d-mannose (1-6) alpha d-mannose. I was using the
pdb2gmx command and 45a3 forcefield .
Showing the fatal error:
Atom O in residue ADE 1 not found in rtp entry with 25 atoms
Just a quick look at the ffG45a3.rtp shows that there is an entry for ADE,
however the ADE entry is for Adenine.
For help with your problem check out:
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
Tom
--On Friday, September 14, 2007
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