[gmx-users] bond managment in grompp
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Mar 22 06:21:02 CET 2012
On 22/03/2012 5:13 AM, francesco oteri wrote:
> Hi Mark,
> these are the involved residues extracted by the .top (CSA and CSB are
> cysteines with modified partial charges):
>
> ; residue 62 CSB rtp CSB q -0.5
> 1010 NH1 62 CSB N 1010 -0.47 14.007
> ; qtot 0.53
> 1011 H 62 CSB HN 1011 0.31 1.008
> ; qtot 0.84
> 1012 CT1 62 CSB CA 1012 0.07 12.011
> ; qtot 0.91
> 1013 HB 62 CSB HA 1013 0.09 1.008
> ; qtot 1
> 1014 CT2 62 CSB CB 1014 -0.05 12.011
> ; qtot 0.95
> 1015 HA 62 CSB HB1 1015 0.051 1.008
> ; qtot 1.001
> 1016 HA 62 CSB HB2 1016 0.051 1.008
> ; qtot 1.052
> 1017 S 62 CSB SG 1017 -0.57 32.06
> ; qtot 0.482
> 1018 C 62 CSB C 1018 0.51 12.011
> ; qtot 0.992
> 1019 O 62 CSB O 1019 -0.51 15.999
> ; qtot 0.482
> ; residue 65 CSA rtp CSA q -0.3
> 1043 NH1 65 CSA N 1043 -0.47 14.007
> ; qtot 0.012
> 1044 H 65 CSA HN 1044 0.31 1.008
> ; qtot 0.322
> 1045 CT1 65 CSA CA 1045 0.07 12.011
> ; qtot 0.392
> 1046 HB 65 CSA HA 1046 0.09 1.008
> ; qtot 0.482
> 1047 CT2 65 CSA CB 1047 -0.03 12.011
> ; qtot 0.452
> 1048 HA 65 CSA HB1 1048 0.08 1.008
> ; qtot 0.532
> 1049 HA 65 CSA HB2 1049 0.08 1.008
> ; qtot 0.612
> 1050 S 65 CSA SG 1050 -0.39 32.06
> ; qtot 0.222
> 1051 C 65 CSA C 1051 0.51 12.011
> ; qtot 0.732
> 1052 O 65 CSA O 1052 -0.51 15.999
> ; qtot 0.222
> ; residue 112 ASN rtp ASN q 0.0
> 1006 NH1 112 ASN N 1006 -0.47 14.007
> ; qtot -4.732
> 1007 H 112 ASN HN 1007 0.31 1.008
> ; qtot -4.422
> 1008 CT1 112 ASN CA 1008 0.07 12.011
> ; qtot -4.352
> 1009 HB 112 ASN HA 1009 0.09 1.008
> ; qtot -4.262
> 1010 CT2 112 ASN CB 1010 -0.18 12.011
> ; qtot -4.442
> 1011 HA 112 ASN HB1 1011 0.09 1.008
> ; qtot -4.352
> 1012 HA 112 ASN HB2 1012 0.09 1.008
> ; qtot -4.262
> 1013 CC 112 ASN CG 1013 0.55 12.011
> ; qtot -3.712
> 1014 O 112 ASN OD1 1014 -0.55 15.999
> ; qtot -4.262
> 1015 NH2 112 ASN ND2 1015 -0.62 14.007
> ; qtot -4.882
> 1016 H 112 ASN HD21 1016 0.32 1.008
> ; qtot -4.562
> 1017 H 112 ASN HD22 1017 0.3 1.008
> ; qtot -4.262
> 1018 C 112 ASN C 1018 0.51 12.011
> ; qtot -3.752
> 1019 O 112 ASN O 1019 -0.51 15.999
> ; qtot -4.262
> ; residue 114 ILE rtp ILE q 0.0
> 1041 NH1 114 ILE N 1041 -0.47 14.007
> ; qtot -4.732
> 1042 H 114 ILE HN 1042 0.31 1.008
> ; qtot -4.422
> 1043 CT1 114 ILE CA 1043 0.07 12.011
> ; qtot -4.352
> 1044 HB 114 ILE HA 1044 0.09 1.008
> ; qtot -4.262
> 1045 CT1 114 ILE CB 1045 -0.09 12.011
> ; qtot -4.352
> 1046 HA 114 ILE HB 1046 0.09 1.008
> ; qtot -4.262
> 1047 CT3 114 ILE CG2 1047 -0.27 12.011
> ; qtot -4.532
> 1048 HA 114 ILE HG21 1048 0.09 1.008
> ; qtot -4.442
> 1049 HA 114 ILE HG22 1049 0.09 1.008
> ; qtot -4.352
> 1050 HA 114 ILE HG23 1050 0.09 1.008
> ; qtot -4.262
> 1051 CT2 114 ILE CG1 1051 -0.18 12.011
> ; qtot -4.442
> 1052 HA 114 ILE HG11 1052 0.09 1.008
> ; qtot -4.352
> 1053 HA 114 ILE HG12 1053 0.09 1.008
> ; qtot -4.262
> 1054 CT3 114 ILE CD 1054 -0.27 12.011
> ; qtot -4.532
> 1055 HA 114 ILE HD1 1055 0.09 1.008
> ; qtot -4.442
> 1056 HA 114 ILE HD2 1056 0.09 1.008
> ; qtot -4.352
> 1057 HA 114 ILE HD3 1057 0.09 1.008
> ; qtot -4.262
> 1058 C 114 ILE C 1058 0.51 12.011
> ; qtot -3.752
> 1059 O 114 ILE O 1059 -0.51 15.999
> ; qtot -4.262
> ; residue 607 CSB rtp CSB q -0.5
> 9693 NH1 607 CSB N 9693 -0.47 14.007
> ; qtot -3.248
> 9694 H 607 CSB HN 9694 0.31 1.008
> ; qtot -2.938
> 9695 CT1 607 CSB CA 9695 0.07 12.011
> ; qtot -2.868
> 9696 HB 607 CSB HA 9696 0.09 1.008
> ; qtot -2.778
> 9697 CT2 607 CSB CB 9697 -0.05 12.011
> ; qtot -2.828
> 9698 HA 607 CSB HB1 9698 0.051 1.008
> ; qtot -2.777
> 9699 HA 607 CSB HB2 9699 0.051 1.008
> ; qtot -2.726
> 9700 S 607 CSB SG 9700 -0.57 32.06
> ; qtot -3.296
> 9701 C 607 CSB C 9701 0.51 12.011
> ; qtot -2.786
> 9702 O 607 CSB O 9702 -0.51 15.999
> ; qtot -3.296
> ; residue 610 CSA rtp CSA q -0.3
> 9732 NH1 610 CSA N 9732 -0.47 14.007
> ; qtot -3.766
> 9733 H 610 CSA HN 9733 0.31 1.008
> ; qtot -3.456
> 9734 CT1 610 CSA CA 9734 0.07 12.011
> ; qtot -3.386
> 9735 HB 610 CSA HA 9735 0.09 1.008
> ; qtot -3.296
> 9736 CT2 610 CSA CB 9736 -0.03 12.011
> ; qtot -3.326
> 9737 HA 610 CSA HB1 9737 0.08 1.008
> ; qtot -3.246
> 9738 HA 610 CSA HB2 9738 0.08 1.008
> ; qtot -3.166
> 9739 S 610 CSA SG 9739 -0.39 32.06
> ; qtot -3.556
> 9740 C 610 CSA C 9740 0.51 12.011
> ; qtot -3.046
> 9741 O 610 CSA O 9741 -0.51 15.999
> ; qtot -3.556
> ; residue 615 NI rtp NI q +0.4
> 9786 NI 615 NI NI 9786 0.4 58.6934
> ; qtot -3.926
> ; residue 616 CN rtp CN q -0.5
> 9787 C 616 CN C1 9787 0.11 12.011
> ; qtot -3.816
> 9788 N 616 CN N1 9788 -0.61 14.007
> ; qtot -4.426
> ; residue 617 CN rtp CN q -0.5
> 9789 C 617 CN C1 9789 0.11 12.011
> ; qtot -4.316
> 9790 N 617 CN N1 9790 -0.61 14.007
> ; qtot -4.926
> ; residue 618 CO rtp CO q -0.1
> 9791 C 618 CO C1 9791 0.22 12.011
> ; qtot -4.706
> 9792 O 618 CO O1 9792 -0.294 15.999
> ; qtot -5
>
>
> While this are the bonds I am referring:
>
> 1017 9786 1
> 1050 9786 1
> 9700 9786 1
> 9739 9786 1
> 1012 9786 1 *
> 1015 9786 1 *
> 1016 9786 1 *
> 1045 9786 1 *
> 1048 9786 1 *
> 1049 9786 1 *
> 9695 9786 1 *
> 9698 9786 1 *
> 9699 9786 1 *
> 9734 9786 1 *
> 9737 9786 1 *
> 9738 9786 1 *
> 9786 9787 1
> 9786 9789 1
> 9786 9791 1
>
> The bonds with the * are what I call fake. i.e the couple 1012 9786
> involves a bond between the nickel atom and an hydrogen.
> This couple, as well as the other fake couples, disappears in the .tpr
> file an interestingly pdb2gmx doesn't signal them.
Your atom numbering is non-unique, so this may be confusing something.
Try pdb2gmx -renumber, and/or feeding the renumbered .gro file into a
second run of pdb2gmx. Also, providing your specbond.dat would help when
seeking answers about how it works...
Mark
>
>
> If the phenomena is not yet known, I can give you the data I used to
> generate the .top and .tpr.
>
> Francesco
>
> Il giorno 21 marzo 2012 16:18, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> ha scritto:
>
> On 22/03/2012 1:46 AM, francesco oteri wrote:
>> Dear gromacs user,
>> I noted a strange behavior in topology generation workflow.
>>
>> I have a protein whose active site contains a Ni atom linked to 4
>> Cys.
>> I inserted the 4 bonds by specbonds.dat. When I run pdb2gmx, I
>> have inspected
>> the Linking messages and they fit with the expected topology, I
>> mean pdb2gmx
>> correctly detects the four bonds nickel-sulphur.
>> So I run grompp and the topol.tpr has been correctly generated.
>>
>> Then I compared topol.top and topol.tpr bonds and I noticed that
>> in topol.top there a lot
>> of fake-bonds, i.e Ni-hydrogen, Ni-Carbonium.
>
> Can you show an example of what you interpret as a fake bond?
>
> Mark
>
>
>>
>> I dumped topol.tpr through gmxdump, and I noticed that these
>> bonds are no more present
>> and only "right" bonds are present.
>>
>> So, I am wondering why the fake bonds are inserted in topol.top
>> and how grompp detectes
>> these bonds.
>>
>>
>> Francesco
>>
>>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto: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
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120322/9e94a5bb/attachment.html>
More information about the gromacs.org_gmx-users
mailing list