Hi David,
It’s been a while since I’ve played around with Mol2 files, but if memory serves that would be counterproductive because if they exist in separate molecule records then they exist in two separate universes (and are only in one file for the sake of convenience, like when doing high-throughput virtual screening or something). They will need to be in a single molecule record. However, you can change the numbering so that the EDTA molecule is a separate substructure and so forth. I can’t remember how many residues (i.e., substructures) one would split a G3.5 PAMAM into, but supposing for the sake of argument it’s 100, EDTA would then need to be the 101st substructure.
I’ve simulated dendrimers with additional small molecules (e.g., ammonium ions) and large molecules (proteins or second dendrimers) before, so I can recall grappling with this problem.
Also, have a look at what Lachele said. You may be able to load the two molecules in from separate files (i.e., one file containing your dendrimer and another containing EDTA) and use LEaP to combine them into one single universe.
Cheers,
Ben
> On 13/10/2015, at 8:02 AM, David Eugene Jones <davide.jones.utah.edu> wrote:
>
> 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 - 12:30:06 PDT
