[gmx-users] Use pdb file generated with Maestro, in Gromacs

bio hpc biohpc2015 at gmail.com
Wed Mar 30 12:27:17 CEST 2016


we have created some protein pdb files with Maestro. When we try to un an MD simulation with gromacs, we get errors like:

>> Atom HD11 in residue ASN 5 was not found in rtp entry ASN with 14 atoms

I tried to find a solution and it seems that internal gromacs dictionary for hydrogens is different from the one from Maestro and other formats. It seems, from what I read, that one must convert all hydrogen types to Gromacs format. Is is there any script that can do this automatically?

Of course, there is the option “ignore hydrogens”, but this would be bad for us, since we need some histidines in the binding site, and so on.


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