OK - as previously mentioned this tutorial is unfortunately out of
date, so you'll have to do a bit extra - it's not impossible though.
First, if you haven't already you should read the introductory chapter
for LEaP in the Amber 16 manual to become familiar with how LEaP does
things. LEaP works with units - to see a list of what units are loaded
type 'list' at the LEaP command prompt. If you load
leaprc.protein.ff14SB, you'll see a lot of amino acid residue units
(e.g. ALA, TRP, etc), but no solvent. That's because solvent/ions are
now loaded via leaprc.water.X files. So just prior to the 'solvatebox'
command, type
source leaprc.water.tip3p
Then type 'list' - you should now see TIP3PBOX listed as a unit (among
other things like ions). Now your 'solvatebox' command should work.
Hope this helps,
-Dan
On Thu, Jul 7, 2016 at 9:13 AM, Corum, Katharine W
<katharine-corum.uiowa.edu> wrote:
>
> Hi,
>
>
> I am using this tutorial from the website: http://ambermd.org/tutorials/advanced/tutorial2/section1.htm
>
>
> I attached the pdb file that goes with the tutorial. I do not have an output file yet as I have not reached that point. I just have an error with my commands.
>
>
> According to the tutorial in order solvate the box the command takes 3 mandatory arguments and 1 optional argument in the form of:
>
>
> solvatebox solute solvent buffer ["iso"] [closeness]
>
>
> This tutorial uses a box of TIP3P water so my command is:
>
>
> solvatebox NMA TIP3PBOX 15
>
>
> However, when I type this in I get a message of:
>
>
>> solvatebox NMA TIP3PBOX 15
>
> solvateBox: Argument #2 is type String must be of type: [unit]
>
> usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
>
>
> Thanks for the help!
>
> Amber Tutorials - A2 Section 1<http://ambermd.org/tutorials/advanced/tutorial2/section1.htm>
> ambermd.org
> A tutorial on running coupled potential Quantum Mechanics / Molecular Mechanics (QM/MM) simulation s using AMBER - Section 1
>
>
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Thursday, July 7, 2016 10:03:53 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Amber16 tutorials
>
> Hi,
>
> It would be better if you posted your entire leap input and output -
> otherwise we have to guess at what is going wrong.
>
> -Dan
>
> On Thu, Jul 7, 2016 at 8:54 AM, Corum, Katharine W
> <katharine-corum.uiowa.edu> wrote:
>> Hi,
>>
>>
>> I used this command...
>>
>>
>> NMA = loadpdb NMA_skeleton.pdb
>>
>> ________________________________
>> From: Hirdesh Kumar <hirdesh.iitd.gmail.com>
>> Sent: Thursday, July 7, 2016 9:52:20 AM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] Amber16 tutorials
>>
>> how did you load your protein??
>> NMA = loadpdb xyz.pdb
>>
>> Is it NMA? or some other variable?
>>
>> *?*
>>
>> On Thu, Jul 7, 2016 at 4:43 PM, Corum, Katharine W <
>> katharine-corum.uiowa.edu> wrote:
>>
>>> Hi, I am stuck on this tutorial again. The command solvatebox NMA TIP3PBOX
>>> 15 does not work. The terminal says...
>>>
>>>
>>> > solvatebox NMA TIP3PBOX 15
>>>
>>> solvateBox: Argument #2 is type String must be of type: [unit]
>>>
>>> usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
>>>
>>>
>>> Thanks!
>>>
>>>
>>> ________________________________
>>> From: Corum, Katharine W
>>> Sent: Wednesday, July 6, 2016 4:16:06 PM
>>> To: AMBER Mailing List
>>> Subject: Re: [AMBER] Amber16 tutorials
>>>
>>>
>>> Thank you!
>>>
>>> ________________________________
>>> From: Hai Nguyen <nhai.qn.gmail.com>
>>> Sent: Wednesday, July 6, 2016 4:14:49 PM
>>> To: AMBER Mailing List
>>> Subject: Re: [AMBER] Amber16 tutorials
>>>
>>> hi,
>>>
>>> You need to download NMA_skeleton.pdb to your computer. There is a link in
>>> the webpage: http://ambermd.org/tutorials/advanced/tutorial2/section1.htm
>>>
>>> Also, in that page, change
>>>
>>> $AMBERHOME/bin/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff14SB
>>>
>>> to
>>>
>>> $AMBERHOME/bin/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.protein.ff14SB
>>>
>>> Hai
>>>
>>> On Wed, Jul 6, 2016 at 5:07 PM, Corum, Katharine W <
>>> katharine-corum.uiowa.edu> wrote:
>>>
>>> > Hi! I am new to Amber. I have just installed Amber16. Are there any
>>> > tutorials that work for Amber16? I have been trying to do tutorials but
>>> > keep getting stuck since they are only updated for Amber15. I am
>>> interested
>>> > in all tutorials, especially QM/MM ones.
>>> >
>>> >
>>> > I would love to do this tutorial but I keep getting a message saying
>>> there
>>> > is no NMA_skeleton.pdb file. Any help would be greatly appreciated!
>>> >
>>> >
>>> > Thanks!
>>> >
>>> > Katie
>>> >
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 07 2016 - 08:30:05 PDT
