Re: [gmx-users] pdb2gmx-4.5 treats DNA as protein (and fails)

So, anybody knows why it does that or how to deal with nucleic acids? I only saw one similar question asked recently (with different error) which was also left without answer. Maiki wrote: Hi, I'm trying to convert protein-DNA complex using pdb2gmx with gromos53a6.ff $ pdb2gmx -f del.pdb -o

Re: [gmx-users] pdb2gmx-4.5 treats DNA as protein (and fails)

David van der Spoel wrote: On 2010-08-16 12.34, Maiki wrote: So, anybody knows why it does that or how to deal with nucleic acids? I only saw one similar question asked recently (with different error) which was also left without answer. Not all force fields have complete support for DNA. Try

Re: [gmx-users] pdb2gmx-4.5 treats DNA as protein (and fails)

David van der Spoel wrote: On 2010-08-16 14.44, Maiki wrote: David van der Spoel wrote: On 2010-08-16 12.34, Maiki wrote: So, anybody knows why it does that or how to deal with nucleic acids? I only saw one similar question asked recently (with different error) which was also left without

[gmx-users] pdb2gmx-4.5 treats DNA as protein (and fails)

Hi, I'm trying to convert protein-DNA complex using pdb2gmx with gromos53a6.ff $ pdb2gmx -f del.pdb -o del.gro -p del.top -i del.itp -n del.ndx -ignh In gromacs version 4.5-beta2 the result is: Processing chain 3 'C' (516 atoms, 25 residues) There are 0 donors and 0 acceptors There are 0