hi
sorry 4 not doing it before, right now am doing "Solvate the Box" step in
molecular modelling am using Gromacs 4.5.5 ver
during the first step i.e "creating the topology file ",i tried to create
the topology file by using the command
"pdb2gmx –ignh –ff G43a1 –f 1OMB.pdb –o fws.pdb –p fws.t
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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@ 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
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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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
--
hi,
i checked the .rtp file residues such as DCN,DC5,DGN,DG5,DAN,DA5,DTN,DT5
dint have any phosphate gp but when i tested the .rtp file with a random DNA
pdb file it is producing a topology file.
-ram
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there were two atoms that were new , i provided them in the .rtp file. only
then i ran the command
regards
ram
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HI, everyone
am working on a system consisting of protein-DNA complex,where an protein
comes and binds to the DNA to form a complex. To produce an topology file in
gromacs i gave the command " pdb2gmx -f XXX.pdb -o XXX.gro -p XXX.top -ter
-ignh -ff amber99 " .
its creating the topology files of
when i ran gromacs to produce topology file for a nucleotide sequence it is
showing the above error saying "There is a dangling bond at at least one of
the terminal ends and the force field does not provide terminal entries or
files. Edit a .n.tdb and/or .c.tdb file". i tried giving the starting
my fault, when i ran gromacs to produce topology file for a nucleotide
sequence it is showing the above error "There is a dangling bond at at least
one of the terminal ends and the force field
does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb
file." i tried giving the startin
hi,
recently while working on gromacs i came across this error "There is
a dangling bond at at least one of the terminal ends and the force field
does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb
file." i tried to edit .tdb file by giving the terminal entries but its
n
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