[gmx-users] amb2gmx.pl file
Oliver Grant
olymacfoogal at gmail.com
Sun Dec 26 17:16:56 CET 2010
Hi Xiaodu,
The fudgeLJ under defaults should be 1.0 for GLYCAM. I'm unable to check my
own files right now so can't compare. When you run grompp check in the
output that fudge is set to 1.0. So there will be no protein in your
simulation correct? I think there is a way to do mixed scaling in gromacs
but I haven't looked into it.
Oliver
2010/12/25 gromacs564 <gromacs564 at 126.com>
> Hi Alan , Oliver
> I have obtained the gromacs format files by amb2gmx.pl script, but I
> am not sure if this flies are correct ,
> because all of the [pairs](1-4 interaction) are zero in gromacs top files.
> I don't know whether this files are correct or not.
> Would you give me some advice? Thank your very much.
>
> all the best
> xiaodu
>
> ------------------------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------------------------
> ; lambda.top created by rdparm2gmx.pl Fri Dec 24 10:22:31 CST 2010
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 2 yes 0.5 0.8333
> [ atomtypes ]
> ;name bond_type mass charge ptype sigma epsilon
> HO HO 0.0000 0.0000 A 0.00000e+00 0.00000e+00
> H1 H1 0.0000 0.0000 A 2.47135e-01 6.56888e-02
> OS OS 0.0000 0.0000 A 3.00001e-01 7.11280e-01
> CG CG 0.0000 0.0000 A 3.39967e-01 4.57730e-01
> H2 H2 0.0000 0.0000 A 2.29317e-01 6.56888e-02
> OH OH 0.0000 0.0000 A 3.06647e-01 8.80314e-01
> [ moleculetype ]
> ; Name nrexcl
> solute 3
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB
> 1 HO 1 ROH HO1 1 0.44500 1.000000
> 2 OH 1 ROH O1 2 -0.63900 16.000000
> 3 CG 2 4GA C1 3 0.50900 12.000000
> 4 H2 2 4GA H1 4 0.00000 1.000000
> 5 CG 2 4GA C2 5 0.24600 12.000000
> 6 H1 2 4GA H2 6 0.00000 1.000000
> 7 OH 2 4GA O2 7 -0.71300 16.000000
> 8 HO 2 4GA H2O 8 0.43700 1.000000
> 9 CG 2 4GA C3 9 0.28600 12.000000
> 10 H1 2 4GA H3 10 0.00000 1.000000
> 11 OH 2 4GA O3 11 -0.69900 16.000000
> 12 HO 2 4GA H3O 12 0.42700 1.000000
> 13 CG 2 4GA C4 13 0.25400 12.000000
> 14 H1 2 4GA H4 14 0.00000 1.000000
> 15 CG 2 4GA C5 15 0.28300 12.000000
> 16 H1 2 4GA H5 16 0.00000 1.000000
> 17 OS 2 4GA O5 17 -0.57400 16.000000
> 18 CG 2 4GA C6 18 0.27600 12.000000
> 19 H1 2 4GA H61 19 0.00000 1.000000
> 20 H1 2 4GA H62 20 0.00000 1.000000
> 21 OH 2 4GA O6 21 -0.68200 16.000000
> 22 HO 2 4GA H6O 22 0.41800 1.000000
> 23 OS 2 4GA O4 23 -0.46800 16.000000
> 24 CG 3 0GA C1 24 0.50900 12.000000
> 25 H2 3 0GA H1 25 0.00000 1.000000
> 26 CG 3 0GA C2 26 0.24600 12.000000
> 27 H1 3 0GA H2 27 0.00000 1.000000
> 28 OH 3 0GA O2 28 -0.71300 16.000000
> 29 HO 3 0GA H2O 29 0.43700 1.000000
> 30 CG 3 0GA C3 30 0.28600 12.000000
> 31 H1 3 0GA H3 31 0.00000 1.000000
> 32 OH 3 0GA O3 32 -0.69900 16.000000
> 33 HO 3 0GA H3O 33 0.42700 1.000000
> 34 CG 3 0GA C4 34 0.25400 12.000000
> 35 H1 3 0GA H4 35 0.00000 1.000000
> 36 OH 3 0GA O4 36 -0.71000 16.000000
> 37 HO 3 0GA H4O 37 0.43600 1.000000
> 38 CG 3 0GA C5 38 0.28300 12.000000
> 39 H1 3 0GA H5 39 0.00000 1.000000
> 40 OS 3 0GA O5 40 -0.57400 16.000000
> 41 CG 3 0GA C6 41 0.27600 12.000000
> 42 H1 3 0GA H61 42 0.00000 1.000000
> 43 H1 3 0GA H62 43 0.00000 1.000000
> 44 OH 3 0GA O6 44 -0.68200 16.000000
> 45 HO 3 0GA H6O 45 0.41800 1.000000
> [ bonds ]
> ; ai aj funct r k
> 1 2 1 9.6000e-02 4.6275e+05
> 21 22 1 9.6000e-02 4.6275e+05
> 18 19 1 1.0900e-01 2.8451e+05
> 18 20 1 1.0900e-01 2.8451e+05
> 15 16 1 1.0900e-01 2.8451e+05
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> [ pairs ]
> ; ai aj funct
> 2 6 1
> 1 4 1
> 1 5 1
> 1 17 1
> ~~~~~~~~~~~~~~~~~~~~
> 5 23 1
> 3 11 1
> 3 13 1
> 3 18 1
> 40 44 1
> 36 40 1
> 36 41 1
> 34 44 1
> 32 36 1
> 32 38 1
> 30 40 1
> 30 41 1
> 28 40 1
> 28 32 1
> 28 34 1
> 26 38 1
> 26 36 1
> 24 32 1
> 24 34 1
> 24 41 1
> [ angles ]
> ; ai aj ak funct theta cth
> 2 3 4 1 1.1000e+02 5.0208e+02
> 1 2 3 1 1.0950e+02 4.6024e+02
> 23 24 25 1 1.1000e+02 5.0208e+02
> 20 18 21 1 1.1000e+02 5.0208e+02
> 19 18 20 1 1.0950e+02 3.7656e+02
> ~~~~~~~~~~~~~~~~~~~
> [ dihedrals ]
> ;i j k l func C0 ... C5
> 2 3 5 6 3 0.20920 0.62760 0.00000
> -0.83680 0.00000 0.00000 ;
> 1 2 3 4 3 0.75312 2.25936 0.00000
> -3.01248 0.00000 0.00000 ;
> 1 2 3 5 3 0.75312 2.25936 0.00000
> -3.01248 0.00000 0.00000 ;
> ~~~~~~~~~~~~~~~~~
> [ system ]
> 45 system
> [ molecules ]
> ; Compound nmols
> solute 1
>
> -------------------------------------------------------------------------------------------------
>
>
>
>
>
>
>
>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101226/882e7999/attachment.html>
More information about the gromacs.org_gmx-users
mailing list