On Sat, Dec 31, 2016 at 2:32 AM, The Cromicus Productions
<thecromicusproductions.gmail.com> wrote:
> I tried the following code in cpptraj, but it seems to not be doing
> anything. Any idea of what could I be doing incorrectly?
Not without more information - 'seems to not be doing anything'
doesn't give us a lot to go on. Can you at least provide the output
from cpptraj? I'll try to comment on your input below.
> parm dna-nowater.prmtop
> trajin md-nowater.mdcrd
> rms first :1-24&!.H=
> average crdset
It's not clear to me exactly what you wanted here since you're using
the 'crdset' keyword here as a file name (which in general you
shouldn't do). Make sure you read the manual entry for each command
carefully; 'average crdset' will create a file named 'crdset', while
'average crdset <set name>' will create a COORDS data set that you can
then use as a reference (and hence keep everything in memory).
> createcrd trajj1
> run
> reference crdset
> crdaction trajj1 rms ref crdset :1-24&!.H=
This seems ok (but pay attention to the output to make sure the
correct reference is being used etc). You're RMS-fitting the
coordinates in COORDS set 'traj1' to the reference 'crdset' (again, I
urge you *not* to use keywords as names since it's easy to get
confused).
> createcrd CRD1
> trajout 1.mdcrd mdcrd
> run
This is where you go wrong I suspect. You're specifying 'createcrd'
which is an Action, so it goes into the Action queue. Actions in the
Action queue operate on frames from input trajectories, which in this
case is 'md-nowater.mdcrd' - hence all you are doing is getting the
same trajectory back again. I suspect what you want is to output the
coordinates in the 'traj1' COORDS data set that you previously
RMS-fit. In this case you need to use the 'crdout' command instead of
'crdaction'/'trajout'/'run':
crdout traj1 1.mdcrd
Hope this helps,
-Dan
>
>
>
>
> On Fri, Dec 30, 2016 at 9:23 PM, The Cromicus Productions <
> thecromicusproductions.gmail.com> wrote:
>
>> Thanks! I'm currently playing with that
>>
>> On Fri, Dec 30, 2016 at 4:21 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>>
>>> May be perform best fit RMSD to reference (starting) structure by cpptraj?
>>>
>>> Hai
>>>
>>> On Fri, Dec 30, 2016 at 2:54 PM, The Cromicus Productions <
>>> thecromicusproductions.gmail.com> wrote:
>>>
>>> > Hi everyone,
>>> >
>>> > I would like to know if there is an easy way to remove the motion
>>> > of the center of mass of a molecule after I have obtained the
>>> > trajectory (.mdcrd and .mdvel) files.
>>> >
>>> > Thanks a lot,
>>> >
>>> > Sebastian
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>>
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--
-------------------------
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 Jan 03 2017 - 06:30:02 PST
