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
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>>
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--
-------------------------
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)
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Received on Thu Jul 07 2016 - 08:30:04 PDT
