Using Conda Amber 2017and using Amber 2014Both have the same for this protein .... With other proteins it is fine
What I am using for conda (and it is tested with other smaller pdb):
source leaprc.gaffsource leaprc.protein.ff14SBsource leaprc.water.tip3p
PROT = loadPdb original.pdbcharge PROTaddIons PROT Na+ 0addIons PROT Cl- 0solvatebox PROT TIP3PBOX 14 iso savePdb PROT 14.pdbsaveamberparm PROT 14.top 14.crd
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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Received on Thu Feb 08 2018 - 05:30:02 PST
