Re: AMBER: problem loading mdcrd to VMD

From: <myang.vitamin.uni.cc>
Date: Tue, 30 Nov 2004 13:48:43 -0500

Try loading in your structure (using PDB file) first.
In my memory, VMD will match your crd to the loaded structure.

Good luck.
Mingfeng

On Tue, Nov 30, 2004 at 05:05:57PM -0000, Ru-Zhen Li wrote:
> Dear David and Stefano,
>
> I have loaded the parmtop file before the mdcrd, and loaded it as a file
> for parmtop, and there is PBC information in the mdcrd, but it doesn't
> matter I choose "crd" or "crdbox", the same thing will happen, I tried rst
> file as well, no luck. any other ideas?
>
> at the same time, I am downloading chimera, see if it will work.
>
> Thank you all,
>
> Ruzhen
> ----- Original Message -----
> From: "David Smith" <David.Smith.irb.hr>
> To: <amber.scripps.edu>
> Sent: Tuesday, November 30, 2004 2:19 PM
> Subject: Re: AMBER: problem loading mdcrd to VMD
>
>
> >Dear Ruzhen,
> >
> >There are a few tricks. First you have to load in a parmtop file. You
> >should know if this is a new or old format and then choose "parm" or
> >"parm7" accordingly from the vmd menu.
> >
> >Then you need to load the .mdcrd file not as a new molecule but as a
> >file for the preloaded prmtop. Then you need to know if your .mdcrd file
> >has box information or not and choose "crd" or "crdbox" accordingly.
> >Alternatively, if your file is really a rst file from Amber 7 or 8 you
> >can choose "rst7".
> >
> >Hope this helps.
> >
> >--
> >Dr. David Smith
> >Division of Organic Chemistry and Biochemistry
> >Rudjer Boskovic Institute
> >Bijenicka 54
> >10002 Zagreb, Croatia
> >tel: +385-1-4561252
> >fax: +385-1-4561118
> >
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Received on Tue Nov 30 2004 - 19:53:01 PST
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