Hi Giulia,
This sounds like a question for the NAMD and/or GROMACS listservs. Did you
use any part of the AMBER package in generating these files? If not, then I
don't think anyone here is likely to be of any help.
Regards,
Brian
On Mon, Oct 22, 2012 at 12:11 PM, Giulia <giulia.palermo.iit.it> wrote:
> Dear all,
>
> I have an equilibrated (for c.a. 160 ns) ternary enzyme/DNA/ligand system
> in water in the NVT ensemble.
> This simulations was done with NAMD. Both the enzyme and DNA were treated
> with the last version of the AMBER FF, whereas the ligand was treated with
> the gaff FF.
> Now, starting from the last equilibrated frame, I would like to use
> GROMACS.
> I will maintain the AMBER topologies, but I need the VELOCITIES of the
> last equilibrated point into a readable format (in columns).
>
> Could you please help me in extracting it?
> As I know, NAMD saves the velocities into a .vel file. However, I was not
> able to extract them in readable format.
>
> Thank you very much
> Giulia Palermo
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Brian Radak : BioMaPS
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Received on Mon Oct 22 2012 - 14:00:04 PDT
