[gmx-users] x2top & Encad all-atom force field (vacuum)
darrellk at ece.ubc.ca
darrellk at ece.ubc.ca
Wed Apr 8 22:19:44 CEST 2009
Dear All,
I forgot to change the subject line of my previous post from
"Re:gmx-users Digest, Vol 60, Issue 40" to something more indicative
of my post, so I am resubmitting it with the appropriate subject title.
Please disregard my earlier post.
Please see my questions inline below.
Thanks.
Darrell
>
>Message: 3
>Date: Mon, 06 Apr 2009 20:58:54 +0200
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Subject: Re: [gmx-users] x2top & Encad all-atom force field (vacuum)
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <49DA50EE.8070100 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>darrellk at ece.ubc.ca wrote:
>> Dear All,
>> I am resubmitting my question below as I did not receive a response and
>> am thinking that my previous e-mail was not recognized by the system or
>> missed. Could someone please provide me with an answer to my questions
>> below?
>>
>> Many thanks.
>>
>> Darrell Koskinen
>>
>> On 4/2/2009, "<darrellk at localhost>" <> wrote:
>>
>>>> Date: Wed, 01 Apr 2009 22:38:28 +0200
>>>> From: David van der Spoel <spoel at xray.bmc.uu.se>
>>>> Subject: Re: [gmx-users] x2top & Encad all-atom force field (vacuum)
>>>> not recognizing bonds
>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>> Message-ID: <49D3D0C4.4040206 at xray.bmc.uu.se>
>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>
>>>> darrellk at ece.ubc.ca wrote:
>>>>> Dear All,
>>>>> I have been trying to determine why I am experiencing problems when I run
>>>>> a gromacs file through x2top. I have checked my gromacs file with VMD to
>>>>> ensure that the file is correct and VMD validates that my file is
>>>>> correct as I see the intended structure. Thus, the atoms are indeed
>>>>> located within reasonable distance from each other such that x2top
>>>>> should be recognizing the bonds.
>>>>>
>>>>> Here is an extract from my gromacs file:
>>>>>
>>>>> 2Grph C 1 0.000 0.000 0.000 0.0000 0.0000 0.0000
>>>>> 2Grph C 2 0.071 -0.123 0.000 0.0000 0.0000 0.0000
>>>>> 2Grph C 3 0.071 0.123 0.000 0.0000 0.0000 0.0000
>>>>> 2Grph C 4 -0.142 0.000 0.000 0.0000 0.0000 0.0000
>>>>> 2Grph C 5 -0.000 -0.250 0.000 0.0000 0.0000 0.0000
>>>>> 2Grph C 6 0.210 -0.120 0.000 0.0000 0.0000 0.0000
>>>>>
>>>>> I thought that in order to make x2top work correctly that I would have to
>>>>> modify the files as described in Christopher Stiles website
>>>>> (http://cs86.com/CNSE/SWNT.htm). I made the specified changes to the
>>>>> following files and saved them in my working directory:
>>>>> ffencadv.n2t
>>>>> ffgmx.n2t
>>>>> ffgmxbon.itp
>>>>>
>>>>> I also changed the name of ffgmxbon.itp to ffencadvbon.itp as I read in
>>>>> one post that this file should be renamed as such.
>>>>>
>>>>> After all these changes, I still experience a problem when I run the
>>>>> command:
>>>>> x2top -ff select -f graphene_nm.gro -o graphene_nm.top
>>>>> selecting option 7: Encad all-atom force field, using scaled-down vacuum
>>>>> charges
>>>>>
>>>>> When I run the above command, I receive output telling me that the atoms
>>>>> have 0 bonds. An extract of the output appears below for your reference.
>>>>> Can not find forcefield for atom H-266 with 0 bonds
>>>>> Can not find forcefield for atom H-267 with 0 bonds
>>>>> Can not find forcefield for atom H-268 with 0 bonds
>>>>> Can not find forcefield for atom H-269 with 0 bonds
>>>>> Can not find forcefield for atom H-270 with 0 bonds
>>>>
>>>> Could there still be an error in your gro file, as it seems to contain
>>>> only C, and the error message points to H. x2top might work slightly
>>>> better in 4.0.x. And by the way, this tutorial may be slightly
>>>> confusing. The only thing you need to do is edit the .n2t file
>>>> corresponding to your force field. I don't recall what is supplied in
>>>> 3.3, but in 4.0 it is ffoplsaa.n2t.
>>> My gro file does contain H atoms as well. In my extract of the gro file I
>>> only showed the first few lines of the gro file and these lines only
>>> have C atoms. Note that I receive the same message for the C atoms (i.e.
>>> "Can not find forcefield for atom C-1 with 0 bonds").
>>>
>>> I actually created the files ffencadv.n2t & ffgmx.n2t in my working
>>> directory since the only n2t file I could find in the gromacs directory
>>> was the ffoplsaa.n2t file and the tutorial did not mention the
>>> ffoplsaa.n2t file. Should I be modifying the ffoplsaa.n2t file instead?
>>> If so, can you please provide me some direction on what needs to be
>>> added to this file so that it recognizes the atoms in my graphene
>>> structure as I looked at this file but do not understand what some of
>>> the columns represent.
>>>
>>> Also, I thought that ffoplsaa was to be used for liquids and since my
>>> simulation is in an air environment, I thought that I should be using
>>> the encad force field in a vacuum and should therefore be modifying an
>>> encad n2t file. Please correct me if I am wrong.
>Encad is not made for vacuum. You have to verify your force field
>anyway, for publication purposes. OPLS will work just fine though.
>
>
>>>
>>> Also, could you also please explain the purpose of the n2t file as I
>>> looked in the gromacs manual and see no description of files with the
>>> n2t extension and their purpose.
>Check archive of the mailing list. This tool will be replaced in the
>near future (5.0), therefore there is no documentation.
>
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.
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?
The 4th column which is 12.011 I assume is the atomic mass.
The 5th column is an integer and I read that this integer represents the
number of protons in the molecule, correct?
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?
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
>>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at http://www.gromacs.org/search before posting!
>>>>> Please don't post (un)subscribe requests to the list. Use the
>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>
>>>> --
>>>> 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
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
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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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