??? wrote:
Hi! everyone,
I am simulating a system containing 5 peptides and a popc membrane.When I use
pdb2gmx,I get this warning:
Fatal error:
Atom H1 in residue GLY 38 not found in rtp entry with 5 atoms
while sorting atoms. Maybe different protonation state.
Remove this hydrogen or choose a different protonation state.
Option -ignh will ignore all hydrogens in the input.
My peptide has 37 residues.I think 38residue is another peptide's first
residue.Its chain number is 2 I am writting in pdb file.It is showing that
pdb2gmx
only read one peptide.How I amend my pdb file to make pdb2gmx can read five
peptides? Please help me.Your advice is appreciated.Thank you!
Did you use option -ignh as the error message suggests?
If your chains are all labeled correctly it should work.
Best regards.
wumin
china HuaZhong Normol University
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