Try to use ambpdb with -aatm flag.
On Thu, Oct 28, 2010 at 2:33 PM, aneesh cna <aneeshcna.gmail.com> wrote:
> Dear Amber users,
> I am using Amber 9.0 for simulation of DNA in water.
> When I use ambpdb command in Amber tools 1.4 for converting restart file (
> *.rst ) to pdb file atom names O1P and O2P ( phosphate oxygens) changes to
> OP1 OP2 in the pdb file, even though the topology file I am using contains
> atom name O1P and O2P. But when I use ptraj to convert restart file to pdb
> file, pdb file maintains the same atom naming as found in the topology
> file. What could be the reason for this change in atom names with 'ambpdb'
> command ?
>
>
> Thanks in advance
>
> Sincerely
> Aneesh
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--
Dmitry Nilov,
Lomonosov Moscow State University
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Received on Thu Oct 28 2010 - 04:00:04 PDT
