[gmx-users] the total charge of system is not an integer
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu Mar 31 11:10:20 CEST 2011
Hi Ahmet,
Why would I get angry? :) Sending a reply to the list will not usually
be taken as asking for private tutoring...
As Mark pointed out, you need to get familiar with the format of the
files. That's the first thing you should do if you get to the point of
needing to use non standard topologies. Read the manual, look at
existing files. As for the immediate question, under the [ atoms ]
section is a line indicating which column denotes what. You'd need to
modify the columns 'cgnr' (charge group number) and probably 'charge'.
For finding proper charge groups, in general you best draw your
molecule, with the charges added, and then see which atoms would
almost naturally group together.
TRS.itp:
..
[ moleculetype ]
; Name nrexcl
TRS 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OA 1 TRS O1 1 -0.119 15.9994
2 H 1 TRS H13 1 0.032 1.0080
3 CH2 1 TRS C1 1 0.087 14.0270
4 CCl4 1 TRS C 2 0.055 12.0110
5 CH2 1 TRS C3 2 0.049 14.0270
6 OA 1 TRS O3 2 -0.205 15.9994
Hope it helps,
Tsjerk
2011/3/31 ahmet yıldırım <ahmedo047 at gmail.com>:
> Dear Tsjerk,
>
> I will ask you one thing but please do not get angry (I know you are not a
> private tutor but I need your helps).
>
> How do I apply on the files (EDO.itp and TRS.itp) that you said? (or can you
> suggest a tutorial?)
>
> Thanks
>
> 2011/3/31 Mark Abraham <Mark.Abraham at anu.edu.au>
>>
>> On 31/03/2011 5:18 PM, ahmet yıldırım wrote:
>>
>> Dear users,
>>
>> Before energy minimization step , I performed the preprosessing step using
>> grompp .
>> However, there are two note that :
>>
>> NOTE 1 [file topol.top, line 52]:
>> System has non-zero total charge: -1.500000e+01
>>
>> This is an integer. See
>> http://en.wikipedia.org/wiki/Scientific_notation#E_notation and
>> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>>
>> NOTE 2 [file topol.top]:
>> The largest charge group contains 11 atoms.
>> Since atoms only see each other when the centers of geometry of the
>> charge
>> groups they belong to are within the cut-off distance, too large charge
>> groups can lead to serious cut-off artifacts.
>> For efficiency and accuracy, charge group should consist of a few atoms.
>> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
>>
>> See Tsjerk's email.
>>
>> Mark
>>
>>
>> PS: TRS and EDO are not aminoacid
>>
>> TRS.itp:
>> ..
>> [ moleculetype ]
>> ; Name nrexcl
>> TRS 3
>>
>> [ atoms ]
>> ; nr type resnr resid atom cgnr charge mass
>> 1 OA 1 TRS O1 1 -0.119 15.9994
>> 2 H 1 TRS H13 1 0.032 1.0080
>> 3 CH2 1 TRS C1 1 0.087 14.0270
>> 4 CCl4 1 TRS C 2 0.055 12.0110
>> 5 CH2 1 TRS C3 2 0.049 14.0270
>> 6 OA 1 TRS O3 2 -0.205 15.9994
>> 7 H 1 TRS H33 2 0.019 1.0080
>> 8 NL 1 TRS N 2 0.206 14.0067
>> 9 H 1 TRS H2 2 0.004 1.0080
>> 10 H 1 TRS H3 2 0.004 1.0080
>> 11 H 1 TRS H1 2 0.004 1.0080
>> 12 CH2 1 TRS C2 2 0.050 14.0270
>> 13 OA 1 TRS O2 2 -0.205 15.9994
>> 14 H 1 TRS H23 2 0.019 1.0080
>> ...
>>
>> EDO.itp
>> ...
>> [ moleculetype ]
>> ; Name nrexcl
>> EDO 3
>>
>> [ atoms ]
>> ; nr type resnr resid atom cgnr charge mass
>> 1 OA 1 EDO OAB 1 -0.111 15.9994
>> 2 H 1 EDO HAE 1 0.031 1.0080
>> 3 CH2 1 EDO CAA 1 0.080 14.0270
>> 4 CH2 1 EDO CAC 1 0.080 14.0270
>> 5 OA 1 EDO OAD 1 -0.111 15.9994
>> 6 H 1 EDO HAF 1 0.031 1.0080
>> ...
>>
>> topol.top:
>> ..
>> ; Include water topology
>> #include "gromos43a1.ff/spc.itp"
>> #include "TRS.itp"
>> #include "EDO.itp"
>> ..
>> [ molecules ]
>> ; Compound #mols
>> Protein_chain_A 1
>> Protein_chain_B 1
>> SOL 185
>> SOL 143
>> TRS 1
>> EDO 1
>> SOL 44125
>>
>> Conf.gro:
>> MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
>> 5354
>> 2GLN N 1 1.458 -1.158 0.739
>> 2GLN H1 2 1.520 -1.083 0.763
>> .......
>> 485HOH HW1 5333 0.221 -3.864 -2.291
>> 485HOH HW2 5334 0.303 -3.946 -2.407
>> 1TRS O1 1 -3.812 -0.471 -2.002
>> 1TRS H13 2 -3.865 -0.443 -1.922
>> 1TRS C1 3 -3.672 -0.469 -1.971
>> 1TRS C 4 -3.635 -0.571 -1.863
>> 1TRS C3 5 -3.711 -0.547 -1.731
>> 1TRS O3 6 -3.694 -0.414 -1.679
>> 1TRS H33 7 -3.746 -0.404 -1.594
>> 1TRS N 8 -3.673 -0.705 -1.911
>> 1TRS H2 9 -3.625 -0.725 -1.996
>> 1TRS H3 10 -3.771 -0.707 -1.927
>> 1TRS H1 11 -3.649 -0.774 -1.842
>> 1TRS C2 12 -3.483 -0.573 -1.840
>> 1TRS O2 13 -3.428 -0.445 -1.806
>> 1TRS H23 14 -3.470 -0.412 -1.722
>> 1EDO OAB 1 0.307 -2.792 0.149
>> 1EDO HAE 2 0.390 -2.826 0.104
>> 1EDO CAA 3 0.239 -2.901 0.212
>> 1EDO CAC 4 0.111 -2.851 0.281
>> 1EDO OAD 5 0.144 -2.763 0.388
>> 1EDO HAF 6 0.060 -2.731 0.432
>> 8.13100 7.04165 13.54850 0.00000 0.00000 -4.06550 0.00000
>> 0.00000 0.00000
>>
>> How can I fixed these notes(note 1 and note 2)?
>>
>> Thanks in advance
>> --
>> Ahmet YILDIRIM
>>
>>
>> --
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>
>
>
> --
> Ahmet YILDIRIM
>
> --
> gmx-users mailing list gmx-users at gromacs.org
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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