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
> _______________________________________________
> 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 Fri Jan 22 2010 - 19:00:02 PST
