Dear Daniel,
Thank you a lot for this helpful insight!
I’ll get the velocities from the output restart file and use them with the set of coordinates I’ve chosen even if they don’t exactly match the ones in the restart output file (hoping this won’t cause much trouble).
I’ll use the trajin/out commands from now on. I had figured that cpptraj would be faster than me in finding in which fragment of the trajectory frame 3089 would be. I had to figure it out again by myself anyway in order to use the closest corresponding velocities.
Thank you again for all the information,
Ruth
> On 22 Nov 2016, at 19:28, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 23 2016 - 02:00:02 PST
