[gmx-users] the total charge of system is not an integer
ahmet yıldırım
ahmedo047 at gmail.com
Thu Mar 31 09:17:50 CEST 2011
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
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