Hi,
Amber trajectory files do not contain velocities by default, so any
restart written from a trajectory frame will also not contain velocity
information. Start your MD run with 'irest = 0'.
If you do have velocity information in your trajectory files, it
should be included in the output restart - make sure you're using the
latest version of cpptraj.
Also note that you don't have to load all of your trajectories in
memory to extract a single frame (in fact it's very inefficient to do
so). Just use 'trajin' instead of 'loadcrd' and 'trajout' instead of
'crdout' (specifying 'onlyframes' instead of 'crdframes'), e.g.
parm native2.parm
trajin nat2_md-qm.nc name nat2-0
...
trajout nat2-0 nat2-0_3089.rst restart onlyframes 3089
Hope this helps,
-Dan
On Tue, Nov 22, 2016 at 12:21 PM, Ruth Helena Tichauer <rhtichau.laas.fr> wrote:
> Dear Amber users,
>
> I’ve been performing QM/MM molecular dynamics of a protein and its ligand. Afterwards, I’ve run cluster analysis to identify representative structures and continue the calculations from one of these structures.
>
> In order to do so, I’ve extracted the coordinates of the structure I’ve chosen using the following script in cpptraj:
>
> #Load topology and trajectories
> parm native2.parm
> loadcrd nat2_md-qm.nc name nat2-0
> loadcrd nat-ew2-0_mdqm.nc name nat2-0
> loadcrd nat-ew2-0_mdqm1.nc name nat2-0
> loadcrd nat-ew2-0_mdqm2.nc name nat2-0
> loadcrd nat-ew2-0_mdqm3.nc name nat2-0
> loadcrd nat-ew2-0_mdqm4.nc name nat2-0
> loadcrd nat-ew2-0_mdqm5.nc name nat2-0
> loadcrd nat-ew2-0_mdqm6.nc name nat2-0
> loadcrd nat-ew2-0_mdqm7.nc name nat2-0
> loadcrd nat-ew2-0_mdqm8.nc name nat2-0
> loadcrd nat-ew2-0_mdqm9.nc name nat2-0
> loadcrd nat-ew2-0_mdqm10.nc name nat2-0
> loadcrd nat-ew2-0_mdqm11.nc name nat2-0
> loadcrd nat-ew2-0_mdqm12.nc name nat2-0
> loadcrd nat-ew2-0_mdqm13.nc name nat2-0
> loadcrd nat-ew2-0_mdqm14.nc name nat2-0
> loadcrd nat-ew2-0_mdqm15.nc name nat2-0
> loadcrd nat-ew2-0_mdqm16.nc name nat2-0
> loadcrd nat-ew2-0_mdqm17.nc name nat2-0
> loadcrd nat-ew2-0_mdqm18.nc name nat2-0
> loadcrd nat-ew2-0_mdqm19.nc name nat2-0
> loadcrd nat-ew2-0_mdqm20.nc name nat2-0
> crdout nat2-0 nat2-0_3089.rst restart crdframes 3089,3089
>
> Now that I want to pursue the QM/MM MD adding new residues to the QM region using the restart coordinates obtained with cpptraj and the topology file I was using from the beginning of my calculation, I get the following error message:
>
> ERROR: I could not find enough velocities in
> nat2-0_3089.rst
>
> I guess I’ve made a mistake somewhere (as I’ve never extract coordinates using cpptraj), please help me correct it to continue my simulation.
>
> Thanks in advance,
>
> Ruth
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Nov 22 2016 - 10:30:02 PST
