Hi,
Without knowing exactly what you are trying to do it's difficult to
tell what may be going wrong. Does your trajectory contain box
coordinates (i.e. were you using GB, PME, etc) and is it ASCII
(ioutfm=0) or NetCDF (ioutfm=1)? What format are you using to try and
load the trajectory into VMD? Does the topology you are using in VMD
match the trajectory (i.e. have you stripped waters etc)?
-Dan
On Mon, Apr 22, 2013 at 1:50 PM, Jonathan Gough
<jonathan.d.gough.gmail.com> wrote:
> Thanks Hai,
>
> That worked, but when I load the trajectory, it's a ridiculous mess. Still
> not sure what's wrong. thoughts?
>
>
> On Mon, Apr 22, 2013 at 3:15 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>> Have you tried loading inpcrd as a restart file into VMD?
>>
>> Hai
>>
>>
>> On Mon, Apr 22, 2013 at 11:50 AM, Jonathan Gough <
>> jonathan.d.gough.gmail.com
>> > wrote:
>>
>> > Dear peoples,
>> >
>> > I took a pdb, cleaned it up. loaded it into leap, saved a pdb, saved the
>> > inpcrd and prmtop files.
>> >
>> > When I load the pdb, everything is fine. when I lod the inpcrd and
>> prmtop,
>> > it looks like a single Nitrogen is stretched out into infinity...
>> >
>> > I can't seem to figure out what the deal is. obviously (maybe)
>> attempting
>> > minimization or heating or anything else makes a huge mess.
>> >
>> > Does anyone have any insight as to where I am making the mistake?
>> >
>> > I can provide lots more details if it's not an obvious error.
>> >
>> > Thank,
>> > Jonathan
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Apr 22 2013 - 14:30:04 PDT
