Is it not possible to do something like the following with your
molecules? (substituting pdb for mol2 here because I have pdb's handy
to use for testing)
m1 = loadpdb molecule1.pdb
m2 = loadpdb molecule2.pdb
translate m2 { 0.0 15.0 0.0 } # or however far in whichever direction
mall = combine { m1 m2 }
# optionally add counterions to mall and/or solvate it
saveamberparm mall mall.parm7 mall.rst7
quit
On Mon, Oct 12, 2015 at 2:45 PM, Ben Roberts <ben.roberts.geek.nz> wrote:
> 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
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>
>
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon Oct 12 2015 - 12:30:03 PDT
