Hi
This error is coming due to mismatch in coordinates..I think you didn't
delete chain In the gro file. First make the starting structure properly
On Fri 17 May, 2019, 4:00 AM paul buscemi, wrote:
> Gromacs is telling you what to do.Make a new top file
>
> I do not think you can start a pdb
Hello paulI think you didnt read my question precisely. I omitted one chain and
saved the .pdb. in the new pdb file residue numbers start from 13 while atom
numbers are correct starting from 1. I have 2 ligands in the file and created
the topology without them and then added 'lig1-lig2.itp' in
Gromacs is telling you what to do.Make a new top file
I do not think you can start a pdb from other than position 1 and the top must
match exactly. it is probably more straightforward to delete the chain and
save the pdb. Use pdb2gmx to recreate the top.
good luck
> On 16,May 2019, at 1:1
Hello all
I want to run a simulation of a protein from PDB data bank with a ligand. It
has two chains and I need only chain A. when I delete chain B in CHIMERA and
try to run the simulation, it stops at the gmx_mpi grompp -f ions.mdp -c
solve.pdb -p topol.top -o ions.tpr step with the error of n
On 7/19/14, 11:46 PM, Jonathan Saboury wrote:
Hello,
I am getting an error:
"Fatal error:
number of coordinates in coordinate file (alb-b4ion.pdb, 192933)
does not match topology (alb.top, 201977)"
Number of SOL/water molecules was done automatically, so not sure why .top
is not
Hello,
I am getting an error:
"Fatal error:
number of coordinates in coordinate file (alb-b4ion.pdb, 192933)
does not match topology (alb.top, 201977)"
Number of SOL/water molecules was done automatically, so not sure why .top
is not matching the .pdb.
Here are the commands used: ht
