[gmx-users] the total charge of system is not an integer
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Mar 31 09:30:48 CEST 2011
On 31/03/2011 6:17 PM, ahmet yıldırım wrote:
> 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?)
You'll need to become familiar with the file format, so that you know
what all the columns of data mean, so you know where the charge groups
are specified. Chapter 5 of the manual is your first port of call. If
you have read that and still have questions about detail, please ask on
the list :-)
Mark
> 2011/3/31 Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto: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
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