[gmx-users] OPLS-AA atom types

[Mark Abraham]

On 6/04/2011 1:00 AM, Austin B. Yongye wrote:
> Thanks Justin.
> It still doesn't solve my problem, e.g., there are several instances of CT with diferent opls_??? numbers, but no indication of their environments; they could represent C bonded to 1->4 carbon atoms, etc. There's no way of telling. I contacted one of the opls folks last week, but got no response. So I thought I could enlist the help of gromacs users.

Yes, but you're making it hard to help you by forcing us to guess what 
content you're looking at. Our time is valuable, and you're not making 
it easy for us to give the minimum amount :-) Tell us what file you 
looked at, what you saw (copy and paste), and why it's not useful.

Mark

> But thanks for your responses anyway.
> Austin-
>
> --- On Tue, 4/5/11, Justin A. Lemkul<jalemkul at vt.edu>  wrote:
>
>> From: Justin A. Lemkul<jalemkul at vt.edu>
>> Subject: Re: [gmx-users] OPLS-AA atom types
>> To: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
>> Date: Tuesday, April 5, 2011, 7:32 AM
>>
>>
>> Austin B. Yongye wrote:
>>> Justin:
>>> I am using gromacs version 4.0.2. Several attempts to
>> download current gromacs versions from http://www.gromacs.org/Downloads kept yielding
>> 93.0-byte files. So I re-installed my pre-existing v4.0.2
>> without any problems (>./configure --enable-sse; make;
>> make install).
>>> If you could send me the ffnonbonded.itp file that
>> would be great.
>>
>> You don't need it.  The corresponding file in 4.0.2 is
>> called ffoplsaanb.itp. Newer Gromacs versions have a
>> different directory and naming structure, but the contents
>> of these files is the same.
>>
>> Be aware that there have been dozens (if not hundreds) of
>> usability upgrades, bug fixes, and new features that have
>> been added since 4.0.2.  You would be well-served to
>> try to figure out why you can't download a newer version.
>>
>> -Justin
>>
>>> Austin-
>>>
>>> --- On Tue, 4/5/11, Justin A. Lemkul<jalemkul at vt.edu>
>> wrote:
>>>> From: Justin A. Lemkul<jalemkul at vt.edu>
>>>> Subject: Re: [gmx-users] OPLS-AA atom types
>>>> To: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
>>>> Date: Tuesday, April 5, 2011, 6:06 AM
>>>>
>>>>
>>>> Austin B. Yongye wrote:
>>>>> Thanks Justin.
>>>>> Could you/someone please forward the file? I
>> don't
>>>> have it.
>>>>
>>>> It's part of your Gromacs installation.
>> $GMXLIB/oplsaa.ff/ffnonbonded.itp.
>>>> If you don't have it, then Gromacs wasn't
>> properly
>>>> installed and you won't be able to use whatever
>> force field for which you're designing
>>>> your topologies.
>>>>
>>>> -Justin
>>>>
>>>>> Austin-
>>>>>
>>>>> --- On Tue, 4/5/11, Justin A. Lemkul<jalemkul at vt.edu>
>>>> wrote:
>>>>>> From: Justin A. Lemkul<jalemkul at vt.edu>
>>>>>> Subject: Re: [gmx-users] OPLS-AA atom
>> types
>>>>>> To: "Discussion list for GROMACS users"
>> <gmx-users at gromacs.org>
>>>>>> Date: Tuesday, April 5, 2011, 5:19 AM
>>>>>>
>>>>>>
>>>>>> Austin B. Yongye wrote:
>>>>>>> Hello GROMACS USERS,
>>>>>>> Does any one have a
>> document/manual/link that
>>>>>> describes the name-number atom type
>> mappings
>>>> employed in
>>>>>> opls-aa?
>>>>>> The correspondence between the atom types
>> and
>>>> bonded types
>>>>>> is all contained in ffnonbonded.itp.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>> I would like to build some molecules
>> and
>>>> specify their
>>>>>> parameters, but I see different of numbers
>> for the
>>>> same atom
>>>>>> type name, e.g:
>>>>>>> TYPE NAME
>>>>>>> 135  CT
>>>>>>> 136  CT
>>>>>>> 137  CT
>>>>>>> 157  CT
>>>>>>>
>>>>>>> I can deduce that 135 is CH3-, 136 is
>> R-CH2-,
>>>> and 137
>>>>>> is RRCH- by looking at topology files.
>>>>>>> Thanks,
>>>>>>> Austin-
>>>>>> --
>> ========================================
>>>>>> Justin A. Lemkul
>>>>>> Ph.D. Candidate
>>>>>> ICTAS Doctoral Scholar
>>>>>> MILES-IGERT Trainee
>>>>>> Department of Biochemistry
>>>>>> Virginia Tech
>>>>>> Blacksburg, VA
>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>>
>>>>>> ========================================
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>>>>>>
>>>> -- ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> MILES-IGERT Trainee
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
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>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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