[gmx-users] x2top & Encad all-atom force field (vacuum)

David van der Spoel spoel at xray.bmc.uu.se
Wed Apr 8 22:40:18 CEST 2009 

Justin A. Lemkul wrote:
> 
> 
> darrellk at ece.ubc.ca wrote:
> 
>>
>> As suggested, I searched the mailing list using the keyword "n2t". The
>> search returned 143 results. I read through all the posts but could not
>> find one that explained to me what each column in the the file
>> ffoplsaa.n2t represents. Could you please direct me to the specific post
>> that provides details on what each column represents in the ffoplsaa.n2t
>> file?
>>
>> I am assuming that the first column represents the atom of interest (e.g.
>> C), whose parameters are determined by specification of the descriptor
>> in the second column (e.g. opls_157).
>>
>> Thus, if we had "C opls_157" in n2t file, we would be assigning to C
>> the paramaters associated with carbon in either a CH3, CH2, or alcohol
>> molecule.
>>
> 
> Yes.
> 
>> The 3rd column is a number, for example 0.085. Does this represent the
>> partial charge on the carbon atom in a CH3 or CH2 molecule?
>>
> 
> Yes.
> 
>> The 4th column which is 12.011 I assume is the atomic mass.
>>
> 
> Right again.
> 
>> The 5th column is an integer and I read that this integer represents the
>> number of protons in the molecule, correct?
>>
> 
> Almost.  That number is how many bonds there are involving the atom 
> specified (i.e., how many atoms are connected to the particular 
> reference atom).  You'll note that this number corresponds to the same 
> number of atom entries that follow on the same line.
> 
>> Columns 6 through 13 have an atom followed by a number between 0 and 1.
>> For example, H 0.108.
>>
>> So let us take an example from the n2t file:
>> C opls_157 0.085 12.011 4 H 0.108 H 0.108 H 0.108 O 0.140
>> Does this row mean that we are specifying that if x2top finds C in the
>> .gro file that the carbon atom will be assigned the force field
>> parameters associated with carbon in the molecule CH3O as defined in the
>> opls_157 force field? And, if this is the case, where does one find
>> information about the paramters specified in the opls_157 force field? I
>> searched the internet and the gromacs website but have found no
>> information on the opls_157 force field. And what do the fractions in
>> the above row represent?
>>
> 
> opls_XXX is not a force field, it is an atom type within the OPLS-AA 
> force field.  Brief descriptions of the atom types are found in 
> ffoplsaa.atp.  The fractions look like they define the bond lengths to 
> the appropriate atoms (i.e., 0.108 nm between the reference C and this 
> atom, H).
> 
> If this information is accurate (I think it is); I'll post it to the 
> wiki, if a developer can confirm.  I have only limited experience 
> playing with x2top.
> 

This is as good as it gets.
Note that you always have to check charges and atomtypes, but for a CNT 
it is not a big challenge.


> -Justin
> 
>> Thanks again.
>>
>> Darrell
>>
>>
>>>>> Thanks again in advance.
>>>>>
>>>>> Darrell
>>>>>
>>>>>>> -------------------------------------------------------
>>>>>>> Program x2top, VERSION 3.3.3
>>>>>>> Source code file: x2top.c, line: 206
>>>>>>>
>>>>>>> Fatal error:
>>>>>>> Could only find a forcefield type for 0 out of 270 atoms
>>>>>>> -------------------------------------------------------
>>>>>>>
>>>>>>> Could you please help me resolve this issue?
>>>>>>>
>>>>>>> Thank you in advance for your assistance.
>>>>>>>
>>>>>>> Darrell Koskinen
>>>>>>> _______________________________________________
>>>>>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>>>>> Please search the archive at http://www.gromacs.org/search before 
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>>>>>> -- 
>>>>>> David.
>>>>>> ________________________________________________________________________ 
>>>>>>
>>>>>> David van der Spoel, PhD, Professor of Biology
>>>>>> Dept. of Cell and Molecular Biology, Uppsala University.
>>>>>> Husargatan 3, Box 596,      75124 Uppsala, Sweden
>>>>>> phone:    46 18 471 4205        fax: 46 18 511 755
>>>>>> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
>>>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
>>>>>>
>>>> _______________________________________________
>>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>
>>> -- 
>>> David.
>>> ________________________________________________________________________
>>> David van der Spoel, PhD, Professor of Biology
>>> Dept. of Cell and Molecular Biology, Uppsala University.
>>> Husargatan 3, Box 596,      75124 Uppsala, Sweden
>>> phone:    46 18 471 4205        fax: 46 18 511 755
>>> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 4
>>> Date: Mon, 6 Apr 2009 23:37:55 +0430
>>> From: "Homa Azizian" <hazizian at razi.tums.ac.ir>
>>> Subject: [gmx-users] partial charge on protein
>>> To: gmx-users at gromacs.org
>>> Message-ID: <20090406185828.M79156 at razi.tums.ac.ir>
>>> Content-Type: text/plain;    charset=iso-8859-1
>>>
>>>
>>> Hi
>>> according to my problem about non-neglible magnitude partial charge on
>>> protein, I did not use -missing option with pdb2gmx my command is:
>>> pdb2gmx -ignh -f .pdb -o .pdb -water spce
>>> what should I do to neutralize this charge?
>>> Thank you in advance.
>>> -- 
>>> Tehran University of Medical Sciences
>>> www.tums.ac.ir
>>>
>>>
>>> -- 
>>> This message has been scanned for viruses and
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>>>
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 5
>>> Date: Mon, 06 Apr 2009 15:53:11 -0400
>>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>>> Subject: Re: [gmx-users] partial charge on protein
>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> Message-ID: <49DA5DA7.30004 at vt.edu>
>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>
>>>
>>>
>>> Homa Azizian wrote:
>>>> Hi
>>>> according to my problem about non-neglible magnitude partial charge on
>>>> protein, I did not use -missing option with pdb2gmx my command is:
>>>> pdb2gmx -ignh -f .pdb -o .pdb -water spce
>>>> what should I do to neutralize this charge?
>>> You should probably start over and check carefully for any warnings 
>>> or error
>>> messages.  Which force field are you using?  A charge of 0.08 sounds 
>>> like a
>>> missing hydrogen, but that may or may not be true.
>>>
>>> -Justin
>>>
>>>> Thank you in advance.
>>>> -- 
>>>> Tehran University of Medical Sciences
>>>> www.tums.ac.ir
>>>>
>>>>
>>> -- 
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Graduate Research Assistant
>>> ICTAS Doctoral Scholar
>>> 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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>>> End of gmx-users Digest, Vol 60, Issue 40
>>> *****************************************
>>>
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> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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