Thanks Hai! I think I'm close to getting it, but I'm running into an error:
raise ValueError("must have the same number of atoms")
ValueError: must have the same number of atoms
*********************************************************
This is my python code:
import pytraj as pt
pdb_traj = pt.load('nuc.pdb')
# xyz : 3D array
import numpy as np
f = open('v00.dat')
content = f.readlines()
xyz = np.reshape(content, (-1, 3))
numrows=len(xyz) #These lines were to verify if my matrix was correct
numcols=len(xyz[0])
print("I have", numrows)
print( "rows and also", numcols)
print( "columns")
print(xyz)
pdb_traj.xyz = xyz
pdb_traj.save('vector.pdb')
****************************************************
My pdb file (nuc.pdb) has 632 atoms and my vector file (v00.dat) has
1896=632*3 lines,
so I have no idea why this is giving me an error :(
On Fri, Nov 18, 2016 at 4:06 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> On Fri, Nov 18, 2016 at 4:02 PM, The Cromicus Productions <
> thecromicusproductions.gmail.com> wrote:
>
> > Thanks for the reply! Sorry for the ignorance, but what do you mean by "
> > your_method_to_load_vector_values"?
> > I have a vector.pev file which I get from using nma.nab, getting a file
> > named "vecs" and renaming it to "vector.pev"
> >
>
> I meant you need to write a small function to load vector.pev to 3D array.
>
> Hai
>
>
> >
> > On Fri, Nov 18, 2016 at 1:30 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> > > One simple way to do is to use pytraj (+ Python) ( :D )
> > >
> > > import pytraj as pt
> > > pdb_traj = pt.load('your.pdb')
> > >
> > > # xyz : 3D array
> > > xyz = your_method_to_load_vector_values(...)
> > >
> > > pdb_traj.xyz = xyz
> > > pdb_traj.save('your_new.pdb')
> > >
> > > Hai
> > >
> > > On Fri, Nov 18, 2016 at 1:26 PM, The Cromicus Productions <
> > > thecromicusproductions.gmail.com> wrote:
> > >
> > > > Hi all,
> > > >
> > > > I'm working with normal mode analysis and have been able
> > > > to obtain vector files (.pev) using nma.nab and using the IED add-on
> > > > (http://mccammon.ucsd.edu/ied/) along with the original pdb file
> > > > with the coordinates I can watch the motion in vmd.
> > > >
> > > > Now, how can I obtain a .pdb file from these vectors? Is there a
> simple
> > > > way?
> > > >
> > > > Thanks a lot,
> > > >
> > > > Sebastian
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- application/octet-stream attachment: v00.dat
Received on Fri Nov 18 2016 - 16:30:02 PST
