Hi Ben,
When I first tried to place the two molecules in the same mol2 file, they were in the same molecule record. What is the best way to combine them as two separate molecule records and maintain their individual atom, substructure, etc. records?
Thanks,
David E. Jones
Graduate Student, Department of Biomedical Informatics
THE UNIVERSITY OF UTAH
421 WAKARA WAY, SUITE 140
SALT LAKE CITY, UT 84108
Phone: 801-870-5704
e-mail: davide.jones.utah.edu
________________________________________
From: Ben Roberts [ben.roberts.geek.nz]
Sent: Monday, October 12, 2015 12:45 PM
To: Amber Mailing List
Subject: Re: [AMBER] How do you place two molecules in one water box?
Hi David,
I know that it’s possible to have two or more molecules in the same file, but in separate molecule records. Have you made sure that the dendrimer and the EDTA molecule are in the same molecule record in your mol2?
Cheers,
Ben
> On 13/10/2015, at 7:28 AM, David Eugene Jones <davide.jones.utah.edu> wrote:
>
> Hi,
>
> I am trying to place two molecules (EDTA and G3.5 PAMAM dendrimer) in a single water box to perform a competing molecule study. I am then planning on adding calcium and sodium as the counter-ions. Thus far I have tried two different methods of loading the two molecules into the box. First I manually combined the two molecules into a single mol2 file. Second I tried turning EDTA into a residue and adding it in xLEaP using the addions command. Neither of these methods worked for placing the two molecules in the same water box. I am wondering if anyone has experience with placing two molecules in the same water box and could offer some advice or point me to an appropriate tutorial?
>
> Thanks,
>
>
> David E. Jones
>
> Graduate Student, Department of Biomedical Informatics
> THE UNIVERSITY OF UTAH
> 421 WAKARA WAY, SUITE 140
> SALT LAKE CITY, UT 84108
>
> Phone: 801-870-5704
>
> e-mail: davide.jones.utah.edu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Oct 12 2015 - 12:30:05 PDT
