[gmx-users] pdb2gmx disulfide bond in dimer

s.varriale s.varriale at ibp.cnr.it
Thu Apr 14 12:31:03 CEST 2016

Dear all,
I try to perform a MD simulation of a covalent dimer with gromacs 4.5.4.
I do:
pdb2gmx -f prot.pdb -chainsep ter
and the programme generates a .gro file with disulfide bond.
but when i want to minimize the system, there is an error:

There were 2 inconsistent shifts. Check your topology
Warning: 1-4 interaction between 45 and 387 at distance 8.995 which is 
larger than the 1-4 table size 2.200 nm

if I try to simulate the 2 chains separatly, there is any error.
What can i do?

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