Hello:
I am currently using Amber 11 for this....
best
On 04/18/2012 09:47 PM, Aron Broom wrote:
> hmm, I don't know what else to suggest then. Whenever I've seen the
> behaviour you are noting (the line of coordinates) it was because I
> accidentally opened something in the incorrect format.
>
> That being said, are you using AMBER 12? I've not yet tested AMBER 12, so
> maybe there is just something new about the formatting that is killing
> things.
>
> ~Aron
>
> On Wed, Apr 18, 2012 at 3:35 PM, Brian Radak<radak004.umn.edu> 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
>>>
>>
>>
>> --
>> ================================ Current Address =======================
>> Brian Radak : BioMaPS
>> Institute for Quantitative Biology
>> PhD candidate - York Research Group : Rutgers, The State
>> University of New Jersey
>> University of Minnesota - Twin Cities : Center for Integrative
>> Proteomics Room 308
>> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
>> Department of Chemistry : Piscataway, NJ
>> 08854-8066
>> radak004.umn.edu :
>> radakb.biomaps.rutgers.edu
>> ====================================================================
>> Sorry for the multiple e-mail addresses, just use the institute appropriate
>> address.
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>>
>
>
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Received on Wed Apr 18 2012 - 13:00:05 PDT
