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

[Justin A. Lemkul]

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.

-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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>>>>> --
>>>>> 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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-- 
========================================

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

========================================