; gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
> Lemkul
> Sent: Monday, June 22, 2015 9:39 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Get pdb2gmx not to treat the first nucleotide in
> a chain as 5'
>
>
>
> On 6/22/15 2:36 PM, Pe
Peter
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
> Lemkul
> Sent: Monday, June 22, 2015 9:39 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Get pdb2
nt: Monday, June 22, 2015 9:39 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Get pdb2gmx not to treat the first nucleotide in a
chain as 5'
On 6/22/15 2:36 PM, Peter Stern wrote:
> I have a chain of RNA in complex with a protein.
> The pdb file is missing the first two nucleo
On 6/22/15 2:36 PM, Peter Stern wrote:
I have a chain of RNA in complex with a protein.
The pdb file is missing the first two nucleotides and starts with the third
including the PO2 group.
pdb2gmx identifies this as the 5' terminal nucleotide and tries to create the topology
from rna.rtp usin
I have a chain of RNA in complex with a protein.
The pdb file is missing the first two nucleotides and starts with the third
including the PO2 group.
pdb2gmx identifies this as the 5' terminal nucleotide and tries to create the
topology from rna.rtp using RA5 as the "residue" type.
Thus it doesn
