Re: [gmx-users] pdb2gmx with amber99 can't find an atom in a DNA duplex

2009-09-17 Thread Gunnar Widtfeldt Reginsson
Problem is solved. The atom needed to be called O not O2. Thanks, On Tue, Sep 15, 2009 at 11:29 PM, Justin A. Lemkul wrote: > > > Gunnar Widtfeldt Reginsson wrote: > >> Hi. Can someone please help me. >> >> I am new to Gromacs. I have a 20mer DNA duplex I want to do some MD on. I >> start by mak

Re: [gmx-users] pdb2gmx with amber99 can't find an atom in a DNA duplex

2009-09-15 Thread Justin A. Lemkul
Gunnar Widtfeldt Reginsson wrote: Hi. Can someone please help me. I am new to Gromacs. I have a 20mer DNA duplex I want to do some MD on. I start by making a topology file form the pdb file. When I run pdb2gmx and the amber99 force field I get this fatal error: 'Atom 02 in residue DT 3 not f

[gmx-users] pdb2gmx with amber99 can't find an atom in a DNA duplex

2009-09-15 Thread Gunnar Widtfeldt Reginsson
Hi. Can someone please help me. I am new to Gromacs. I have a 20mer DNA duplex I want to do some MD on. I start by making a topology file form the pdb file. When I run pdb2gmx and the amber99 force field I get this fatal error:'Atom 02 in residue DT 3 not found in rtp entry with 32 atoms while sort