Dear users
I am trying to run pdb2gmx on a protein holding ATP (with gromacs 467 and
gromos43a1p.ff). However I have problem introducing ATP atom names in the input
pdb file, based on the .rtp file of gromos43a1p (for example AO1PA is the name
for an oxygen atom of ATP based on gromos43a1p
Dear Users
I am trying to run pdb2gmx (in gromacs 5.0.5 and by 43a1p.ff) on o modeled
structure holding ATP, water and TPO as hetero atoms. but I am faced with the
following error. I checked all LUE residues (although I have got no residue
with 28215089 number) and I found no missing atom N. I
Dear Users
I am trying to run pdb2gmx (in gromacs 5.0.5 and by 43a1p.ff) on o modeled
structure holding ATP, water and TPO as hetero atoms. but I am faced with the
following error. I checked all LUE residues (although I have got no residue
with 28215089 number) and I found no missing atom N. I
Dear users
I am trying to build the .itp file of a ligand (derived from a crystal
structure and in complex with protein). As I try to submit the molecule at ATB
server, I am supposed to prepare the total charge of my ligand. could you
suggest any straight forward (or non-straight forward)
Dear usersI am trying to calculate the interface/buried surface between two
chains of a multichain protein by gromacs5. should I be using sasa commands? if
so, should I be finding the result of chainA_SASA + chainB_SASA - ((chainA +
chainB)SASA) equation?if so, which groups should I be
dear users
I have an .xtc file regarding an interacting protein/peptide complex. as i
extract a pdb from this trajectory, i find the peptide separated from protein
and in a position very far from it. i derived a pdb from .tpr file, to make
sure that my starting structure is intact compared to
Dear users
i wanted to know if Acpyte generated topologies for a ligand are compatible
with OPLS-AA.ff? i am searching for a reliable topology builder for OPLS-aa
like ATP for gromos53a6.ff so that i can avoid manual approached like using
gaussian .
regards,
Saman
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Gromacs Users mailing
Dear users
i wanted to know if Acpyte generated topologies for a ligand are compatible
with OPLS-AA.ff? i am searching for a reliable topology builder for OPLS-aa
like ATP for gromos53a6.ff so that i can avoid manual approached like using
gaussian .
regards,
Saman---BeginMessage---
Dear
dear users
I am trying to have several trajectories for one simulated system to check if
my results are reproducible or not. should I be making several .tpr files with
the same pdb file or is there any way I can have several random seeds for the
mud run command? i mean is there any way i can
dear users
i am trying to make a .xtc file from an existing .trr and exclude some frams of
.trr file. should i be using trajconv to cut the trajectory around the
nonwanted frames and fuse the wanteds by trajcat? is there any other way to do
it in a single command?
regards,
saman
--
Gromacs
Hello dears
i am trying to do some analysis on a trajectory by gromos43a1ff. but as i run
pdb2gmx, an error shows up that the HISE residue is not known to this
forcefield. how can i deal with this issue? can i be introducing the parameters
of HISE to gromos43a1? if so, how can i get them and
was not found in rtp entry TYR with 18 atoms
while sorting atoms.
any suggestion on dealing with OXT?
best,
Saman
On Saturday, January 25, 2014 4:27 PM, Justin Lemkul jalem...@vt.edu wrote:
On 1/25/14, 7:18 AM, Saman Shahriyari wrote:
Hello dears i am trying to do some analysis
Dear users
is there any way to retrieve box size and othe properties from .trr or .tpr
file?
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