[gmx-users] CA2+ vs. CA

Arturas a3arzi at vaidila.vdu.lt
Thu Jul 10 13:52:01 CEST 2003

Hello gmx-users,

Possibly got dumb question, so sorry in advance ;)

Got an anzyme with calcium (2+). So i modify my pdb sorce file for
gromacs, pdb2gmx says there is fatal error, because it did not found
Ca2+ ir rtp. pdb2gmx runs successfully with simple 'Ca' i pdb file (as
residue and atom names).

How to enforce to treat calcium as ion (2+), or there is no difference
at all ??   Or, I have found that in topology files heme has name
'HEME', but in PDB files the conventional name is 'HEM'.

Should I modify residue names in PDB files in order to meet the names
in topoly files of gromacs ?? How to treat that situation in proper
way ? 

The only message i foung in gmx archieve is like this:
editconf -f file.pdb -o file.gro

Then edit file.gro and change the names to what ever you like, then use
file.gro as input for pdb2gmx

Best regards,
Arturas Z.                         

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