Dear Gromacs Users,
I'm calculating the 2d-RDF of lipids in the bilayer. I use g_rdf with
the -xy option to calculate the 2d-RDF and I pick the lipids in either
one of the bilayer's leaflets. I also would like to calculate the
coordination number (with -cn option) but i'm not sure if the
normali
Jacob Harvey wrote:
Dear All,
I am having issues editing a .rtp file (ffoplsaa.rtp to be exact). I
want to create a new residue for my system so that I can generate a
topology file using pdb2gmx. This is the code that I have added to the
.rtp file:
[ IMD ]
[ atoms ]
NA opls_557-
Dear All,
I am having issues editing a .rtp file (ffoplsaa.rtp to be exact). I want to
create a new residue for my system so that I can generate a topology file
using pdb2gmx. This is the code that I have added to the .rtp file:
[ IMD ]
[ atoms ]
NA opls_557-.2571
CR opls_558
Jacob Harvey wrote:
Justin,
How do I go about running topolgen on a linux system? There doesn't seem
to be instructions for use, but I'm not familiar with perl scripts. Also
I'd just like to say thank you for all your help. You've been really
good with responding to my e-mail. I know that y
Jacob Harvey wrote:
Thank you for your help Justin. I have corrected my naming problem in
the pdb file. However, I am still getting errors. It does not seem to
recognize the residues. BUT I dont actually have "residues" in my
system, because I am not modeling a protein. So I am not sure what
Thank you for your help Justin. I have corrected my naming problem in the
pdb file. However, I am still getting errors. It does not seem to recognize
the residues. BUT I dont actually have "residues" in my system, because I am
not modeling a protein. So I am not sure what to put in the residue name
Jacob Harvey wrote:
Dear All,
I am trying to use the OPLS-AA force field to model some imidazole
containing compounds. I've noticed that imidazole units are referenced
in the ffoplsaa.atp file as the following:
opls_557 14.00670 ; N1 in imidazole
opls_558 12.01100 ; C2 in imidazol
Hi Jacob,
It looks like your pdb file does not contain any residue names, since
you residue column is filled with the number "2" which I'm guessing
isn't specified as a canonical residue. I'm not sure how you're
generating this PDB file, but if you're doing it by hand, I would
strongly re
Dear All,
I seem to be having issues with the pdb file I wish to use in gromacs. I am
trying to model this system using the OPLS-AA force field however I get the
error
"Fatal error:
Residue '' not found in residue topology database"
I know what this error means but its not naming a specific resi
Dear All,
I am trying to use the OPLS-AA force field to model some imidazole
containing compounds. I've noticed that imidazole units are referenced in
the ffoplsaa.atp file as the following:
opls_557 14.00670 ; N1 in imidazole
opls_558 12.01100 ; C2 in imidazole
opls_559 14.00670 ; N
Dear sir,
I want to pull a small protein molecule (GPI) which is inserted
on the upper layer of the bilayer. So, I applied pull = umbrella, where
umbrella potential is used between center of mass of reference group and
that of pulled group. Now, as I want to pull the protein from the li
Hello gromacs users,
I want to ask a simple thing, which nevertheless is not really clear to me,
but it's sometimes too important. For instance, I have in my molecule
torsinal
angle around a double bond: -C-C(H)=C(H)-C-. The dihedral potential contains
following four parts:
-C-C=C-C-, a U1 fro
nitu sharma wrote:
Hello justin
thanks for ur suggestion . I am trying to do membrane protein simulation
with lipid bilayer . I have pdb file of inserted protein in dmpc lipid
bilayer. But I am facing problem in making topology file for this
system.As u told in previous mail you can't combi
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