Hi Nicholas,
I loaded my prmtop (top) file first and then I loaded the mdcrd. It seems
to show bad connections with unexpected lines when I did that. I will go
through all the links and points you mentioned and verify that I have loaded
the files appropriately. Thank you very much for your quick reply.
Jagdeesh
On Sat, Jan 23, 2010 at 8:06 AM, Nicholas Musolino <musolino.mit.edu> wrote:
> Hi Jagdeesh,
>
> Could I ask, how are you loading your output in order to visualize in NAMD?
> Are you loading any topology information, or just coordinates?
>
> Can I make a couple points:
> 1. The bonding information displayed in VMD can either be automatically
> (heuristically) generated based on the xyz coordinates of the atoms, or,
> depending on what information you load, represent the actual topological
> structure.
> See http://www.ks.uiuc.edu/Research/vmd/current/ug/node26.html:
> > When a coordinate file is loaded by itself (i.e. just a PDB, no PSF), VMD
> uses heuristics to replace missing values that would normally be provided by
> a structure file. If necessary, VMD does a distance-based bond search to
> determine connectivity. A bond is formed whenever two atoms are within
> (R1+R2)*0.6 of each other, where R1 and R2 are the respective radii of
> candidate atoms. If both structure and coordinate files are loaded, no
> approximations or guesses are made.
>
>
> 2. You can load an AMBER parm (prmtop) file using VMD, and then load
> coordinate data in from a trajectory. I often run VMD like this from the
> command line:
> vmd -dispdev text example.prmtop example_run_1.dcd
> where the .dcd is an NAMD trajectory. If VMD does not recognize the
> filetype, you can use either the -parm or -Parm (forget which, case
> sensitive). See this page for more information:
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node204.html
>
> 3. You can load files and disable the automatic bond visualization using
> the "autobonds off" option in the "molecule" command. See this page for
> more information:
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node135.html
>
> 4. If you provide more info about what you're giving to VMD, I may be able
> to help more. I have a lot of experience with LEAP and NAMD/VMD, although
> little with AMBER, so I can't say whether the approach you took in the AMBER
> script makes sense.
>
> Hope these are helpful!
> Nicholas
>
> ---------------------------------------------------------------------------
> Nicholas Musolino
> Ph.D. candidate, Department of Chemical Engineering, MIT
> musolino.mit.edu | 617-253-6675 | Room E19-528
>
> On Jan 22, 2010, at 9:10 PM, Jagdeesh C wrote:
>
> > Dear Amber Users,
> >
> > I built my starting structure and ran a simulation to obtain an
> equilibrated
> > system along the same lines shown in the MM PBSA tutorial section 1. When
> I
> > was visualizing the mdcrd files using VMD I saw that the atoms are
> totally
> > hapazard and randomly connected.
> >
> > minimise hn
> > &cntrl
> > imin=1,maxcyc=1000,ncyc=500,
> > cut=10.0,ntb=1,
> > ntc=2,ntf=2,
> > ntpr=100,
> > ntr=1, restraintmask=':1-23',
> > restraint_wt=2.0
> > /
> >
> > heat hn
> > &cntrl
> > imin=0,irest=0,ntx=1,
> > nstlim=50000,dt=0.002,
> > ntc=2,ntf=2,
> > cut=10.0, ntb=1,
> > ntpr=500, ntwx=500,
> > ntt=3, gamma_ln=1.0,
> > tempi=0.0, temp0=300.0,
> > ntr=1, restraintmask=':1-23',
> > restraint_wt=2.0,
> > nmropt=1
> > /
> > &wt TYPE='TEMP0', istep1=0, istep2=25000,
> > value1=0.1, value2=300.0, /
> > &wt TYPE='END' /
> >
> > Can someone suggest me, which place I am possibly going wrong? I can
> provide
> > more information if necessary. Do I need to give stronger restraints?
> >
> > Thanks,
> > Jagdeesh
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>
>
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Received on Fri Jan 22 2010 - 19:00:03 PST
