I suppose that this is the problem with the visualization Carlos, I'm
using iwarp=1, but I need it (but thanks, at least now I know why this
problem).
I've taken a look to the manual, and now I have differents pdb for
differents frames.
Other thing,
after this MD with AMBER I need use the CPMD program for QMMM
calculations, and for this I need a topology and a coordinate file. Is
for this reason that I want obtain this .crd (or .inpcrd) file, but I
don't find any option with ptraj, and whit Sander I obtain .mdcrd
Any suggestion?
Quoting Carlos Simmerling <carlos.simmerling.gmail.com>:
> you can use vmd to load the entire trajectory directly, and scroll
> through the frames.
> just make sure to image the trajectory first, since it may be that you
> did not set iwrap=1
> and your water has diffused. there is plenty of information about this
> in the archives (including examples) - search for ptraj and image (or
> look in the ptraj manual)
>
>
> On Fri, Feb 6, 2009 at 5:48 AM, <vallespardojl.chem.leidenuniv.nl> wrote:
>> Dear amber users,
>>
>> I've made a MD job. The output file seems correct, but when I check the
>> final structure in the restart file with the VMD (.rst file + .top file)
>> there are something wrong (appears a hole in the solvatation cubic box).
>> For this reason I want extract different frames from the mdcrd file. What is
>> the best option for made this? Can I visualize the frames directly with
>> ptraj? or I create a crd file with ptraj, and then I visualize this file
>> with VMD?
>>
>> A lot of thanks,
>>
>> José Luis
>>
>>
>> _______________________________________________
>> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 11 2009 - 01:16:21 PST
