Date: Fri, 9 Feb 2018 09:02:16 -0500
Hi,
It seems to work fine for me (see attached). Here's what I did. First
I preprocessed with pdb4amber:
pdb4amber -i original.pdb -o amber.pdb -y
Then I used the following leap input:
source leaprc.protein.ff14SB
source leaprc.water.tip3p
m = loadpdb amber.pdb
solvatebox m TIP3PBOX 15.0 iso
saveamberparm m test.parm7 test.rst7
quit
Note that if you don't want to keep the waters in the PDB you can use
the '-d' command line flag. Hope this helps,
-Dan
On Thu, Feb 8, 2018 at 11:32 AM, Ahmed Mashaly <mashaly_1988.yahoo.com> wrote:
> And this is the molecule if you wanna tryhttps://drive.google.com/open?id=17CfGKuPlrEjMbml48EO_ka1rJK2b6SqZ
>
>
> Kind Regards,Ahmed
>
>
>
> From: Daniel Roe <daniel.r.roe.gmail.com>
> To: Ahmed Mashaly <mashaly_1988.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
> Sent: Thursday, February 8, 2018 1:14 PM
> Subject: Re: [AMBER] solvatebox iso error
>
> Hi,
>
> What version of AmberTools are you using? Also, can you provide all of
> the commands you are giving to leap? I can't seem to reproduce your
> error.
>
> -Dan
>
>
>
> On Wed, Feb 7, 2018 at 1:10 PM, Ahmed Mashaly <mashaly_1988.yahoo.com> wrote:
>> Hi
>> When I use this command solvatebox prot TIP3PBOX 15 iso
>> I have this weird boxhttps://drive.google.com/open?id=1xslAwz-0YnDAtfU-u2AZ68JuozKfpzgF
>>
>> It works fine without iso, but I need a cubic box, not a rectangular one!! Kind Regards,Ahmed
>>
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>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
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>
>
>
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-- ------------------------- Daniel R. Roe Laboratory of Computational Biology National Institutes of Health, NHLBI 5635 Fishers Ln, Rm T900 Rockville MD, 20852 https://www.lobos.nih.gov/lcb
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