[gmx-users] x2top & Encad all-atom force field (vacuum)
Justin A. Lemkul
jalemkul at vt.edu
Wed Apr 8 23:22:48 CEST 2009
David van der Spoel wrote:
> 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.
>
For those who come looking, the wiki has been updated:
http://wiki.gromacs.org/index.php/Manual:x2top_4.0.3
-Justin
>
>> -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
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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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>>>> believed to be clean.
>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> 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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>>
>
>
--
========================================
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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