Hi Ella,
There is no repository of MDL files.
prepdat.pl was written to build MDL files for common solvent and co-solvents in the Amber force field. If you have or can create parm7 and rst7 files of your molecules, it should be straightforward to adapt the script to build MDL files from them. The buildParm() function should do this. I’d be happy to help you adapt it if you contact me off list.
If you can’t create parm7 and rst7 files, then you’ll have to write your own script. The file format should be online soon. It is a fairly simple format but watch out for the LJSIGMA parameter, which is really Rmin/2.
Tyler
> On Nov 18, 2015, at 4:51 AM, Ella Gale <ella.gale.gmail.com> wrote:
>
> Hi Tyler,
>
> I'm after DMSO to start with, and some ionic liquids ([EMIM][OAc]). I'm
> trying to figure out the method to generate the .mdl files, so I can easily
> make any liquid, and I don't want to edit the files by hand as that is how
> errors creep in.
>
> Do you know if there are any repositories for .mdl files?
>
> I found a perl script in the dat/rism/model/ folder of the amber install,
> but I'm having trouble figuring out which files that needs as input
>
> Regards
>
> Ella
>
> On Tue, Nov 17, 2015 at 8:56 PM, Tyler Luchko (Lists) <
> tluchko.lists.gmail.com> wrote:
>
>> Hi Ella,
>>
>> I’m afraid that the manual and $AMBERHOME/dat/rism1d/mdl are not up to
>> date on this matter.
>>
>> What solvent molecules do you need MDL files for? There may be some that
>> are already prepared that meet your needs.
>>
>> I’ll try and get the RISM formats online in the next day or so.
>>
>> Tyler
>>
>>> On Nov 17, 2015, at 7:22 AM, Ella Gale <ella.gale.gmail.com> wrote:
>>>
>>> Dear all,
>>>
>>> I want to run some simple 1DRISM calculations using 'rism1D'
>>>
>>> The manual (copied below) says that you need .mdl file, but does not give
>>> any instructions on how to build them and link provided (which is
>> supposed
>>> to explain this) doesn't. In the $AMBERHOME/dat/rism1d/mdl is a perl
>> script
>>> which requires .parm7 and .rst7 files.
>>>
>>> My question: How do I create .mdl files for use with 1DRISM?
>>>
>>> Taken from the manual: 1D-RISM calculations require details of the some
>>> bulk properties of the solvent, such as temperature and dielectric
>>>
>>> constant, and an explicit model of the molecular components. These are
>> read
>>> in from one or more .mdl
>>>
>>> files, depending on the composition of the solvent. Several .mdl files
>> are
>>> included in the Amber11 distribution
>>>
>>> and can be found in $AMBERHOME/dat/rism1d/mdl. These include many of the
>>> explicit models for solvent and
>>>
>>> ions used with the Amber force fields. Other solvents models may be used
>> by
>>> creating appropriate MDL files. See
>>>
>>> http://ambermd.org/formats.html for format details.
>>>
>>>
>>> Thanks in advance,
>>>
>>>
>>> Regards
>>>
>>>
>>> Ella
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
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Received on Wed Nov 18 2015 - 10:00:03 PST
