darre...@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
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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
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------------------------------
Message: 4
Date: Mon, 6 Apr 2009 23:37:55 +0430
From: "Homa Azizian" <haziz...@razi.tums.ac.ir>
Subject: [gmx-users] partial charge on protein
To: gmx-users@gromacs.org
Message-ID: <20090406185828.m79...@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
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------------------------------
Message: 5
Date: Mon, 06 Apr 2009 15:53:11 -0400
From: "Justin A. Lemkul" <jalem...@vt.edu>
Subject: Re: [gmx-users] partial charge on protein
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <49da5da7.30...@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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========================================
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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