Hi guys:
thank you very much for kind reply.
I use command:
vmd bm.prmtop -rst7 bm.inpcrd
and it seems to be OK in the VMD view. However, I still have the same
problem to open the periodic cell: all x, y, z are in the same
place..... I don't know why.
On 04/18/2012 09:35 PM, Brian Radak wrote:
> This might actually be a question for the VMD guys, but I'll add my 2 cents.
>
> First of all, in general AMBER rst7 files do not necessarily contain
> velocity information (see the AMBER formats page).
>
> In my experience the VMD plugins for the inpcrd format are a bit shaky
> (although I think this is really a matter of incorrect expectation). They
> sometimes read the number of atoms as the x coordinate of the first atom,
> which is why you'll see one atom way outside the box with a long bond. I
> don't know if this is because the format was changed at some point or
> what.
>
> In any event, you can almost always open inpcrd files as the rst7 format.
> You can force VMD to do that by just naming all of your files with the rst7
> extension, or use the -rst7 flag on the command line. You can of course
> select AMBER restart 7 from the GUI too, but I rarely use the GUI for
> loading lots of files.
>
> Regards,
> Brian
>
>
>
> On Wed, Apr 18, 2012 at 3:21 PM, Aron Broom<broomsday.gmail.com> wrote:
>
>> First, open your inpcrd file and go to the bottom and see if you actually
>> have a line describing the periodic conditions (lengths and angles). If
>> so, it's probably the way you opened it, an inpcrd file is not an AMBER
>> restart file, the restart file contains velocity information also. You
>> should open it as AMBER periodic coordinates, or something of the sort.
>> All those options should be right next to each other in VMD, so it's
>> surprising that you would have chosen the restart.
>>
>> Also, I think you want to open the prmtop first, and then load the inpcrd
>> into that.
>>
>> ~Aron
>>
>> On Wed, Apr 18, 2012 at 3:16 PM, Albert<mailmd2011.gmail.com> wrote:
>>
>>> Dear:
>>> I've built an md system with tleap by following command:
>>>
>>> tleap -s -f leaprc.ff99SBildn
>>> source leaprc.gaff
>>> loadamberparams ligand_AC.frcmod
>>> loadoff ligand_AC.lib
>>> mol = loadpdb complex.pdb
>>> solvatebox mol TIP3PBOX 11.0
>>> charge mol
>>> addions mol Na+ 42
>>> addions mol Cl- 30
>>> charge mol
>>> set default FlexibleWater on
>>> saveamberparm mol bm.prmtop bm.inpcrd
>>>
>>> After than I open the solvated system in VMD:
>>>
>>> new molecule --> bm.inpcrd (amber 7 restart)
>>> load --> bm.prmtop (amber7 parm)
>>>
>>> everything seems to be ok in VMD molecule viewer window. However, when I
>>> try to open the periodic cell, nothing happen.... what I found is: all
>>> Self, +x +y, +z are in the same position which responsible for that I
>>> see "no periodic" cell because they overlap with each other......
>>>
>>> I also try to type
>>>
>>> pbc box
>>>
>>> in VMD terminal, and it said:
>>>
>>> -error Suspicious pbc side length (a=0.000000 b=0.000000 c=0.000000).
>>> Have you forgotten to set the pbc parameters?
>>>
>>> Does anybody have any idea what happen?
>>>
>>> thank you very much
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Wed Apr 18 2012 - 13:30:03 PDT
