Aha, it works on pdb file! Thanks MingFeng.
----- Original Message -----
From: <myang.vitamin.uni.cc>
To: <amber.scripps.edu>
Sent: Tuesday, November 30, 2004 6:48 PM
Subject: Re: AMBER: problem loading mdcrd to VMD
>
> 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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>>
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> --
> Life sucks, but we can change it.
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Received on Tue Nov 30 2004 - 23:53:00 PST
