[gmx-users] RENUMTOP
David
spoel at xray.bmc.uu.se
Sun Feb 15 07:27:00 CET 2004
On Sun, 2004-02-15 at 00:42, Martina Bertsch, PhD wrote:
> Greetings.
>
> I need to perform simulated annealing of the receptor-ligand complex in
> vacuum as described in my previous e-mails.
>
> I prepared the rec.gro and rec.top using pdb2gmx by selecting ffG43b1. I
> also prepared the lig_vac.itp manually using the ffG43a1 parameters, as
> the PRODRG server only outputs the ffgmx itp. The lig_vac.itp is enclosed.
>
> Next, I merged the rec.top and lig_vac.itp into one file, rec_lig.top,
> as described in Anton's e-mail, dated December 1, 2003:
>
> 1) I labeled all lig atom numbers (in atoms, bonds, angles, etc) with an 'm' after the atom numbers.
> 2) I merged all sections separately (i.e., appended lig atoms to protein atoms, lig bonds to protein bonds, etc).
> 3) I ran the 'renumtop' script on the merged topology; it did re-assign the right atom numbers (in atoms, bonds, angles, etc) for all lig
> atoms added in step 2.
>
why? is there a covalent bond between your ligand and protein? otherwise
this is not necessary at all.
> However, when I ran grompp with the new merged and renumbered top file, I got the following message:
>
> Fatal error: Invalid bond type 0
>
> I suspect I am missing something in my lig_vac.itp, but I am completely new to building ffG43a1/b1 ligand itp files "from scratch".
>
Doesnn't it say on which line in the topology things go wrong?
The simplest test for your topology is to minimize the ligand separately
of the protein, and in the process get rid of possible error in your
ligand top.
> Any help will be greatly appreciated.
>
>
> Best regards,
> Martina Bertsch, Ph.D.
>
> [ moleculetype ]
> ;name nrexcl
> DRG 3
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1m CH3 285 DRG CAO 1 0.000 15.035
> 2m C 285 DRG CAM 1 0.380 12.011
> 3m O 285 DRG OAN 1 -0.380 15.9994
> 4m N 285 DRG NAL 2 -0.280 14.0067
> 5m H 285 DRG HAB 2 0.280 1.008
> 6m CH2 285 DRG CAK 3 0.000 14.027
> 7m CH2 285 DRG CAJ 3 0.000 14.027
> 8m C 285 DRG CAA 4 -0.140 12.011
> 9m C 285 DRG CAC 4 0.000 12.011
> 10m CR1 285 DRG CAF 5 0.000 13.019
> 11m C 285 DRG CAH 5 0.100 12.011
> 12m OA 285 DRG OAP 6 -0.100 15.9994
> 13m CH3 285 DRG CAQ 6 0.000 15.035
> 14m CR1 285 DRG CAI 7 0.000 13.019
> 15m CR1 285 DRG CAG 7 0.000 13.019
> 16m C 285 DRG CAE 8 0.000 12.011
> 17m NR 285 DRG NAD 8 -0.050 14.0067
> 18m H 285 DRG HAA 8 0.190 1.008
> 19m CR1 285 DRG CAB 8 0.000 13.019
> [ bonds ]
> 1m 2m gb_26
> 2m 3m gb_4
> 2m 4m gb_9
> 4m 5m gb_2
> 4m 6m gb_20
> 6m 7m gb_26
> 7m 8m gb_14
> 8m 19m gb_9
> 8m 9m gb_9
> 19m 17m gb_9
> 17m 18m gb_2
> 17m 16m gb_9
> 16m 9m gb_15
> 9m 10m gb_15
> 10m 11m gb_15
> 11m 14m gb_15
> 14m 15m gb_15
> 15m 16m gb_15
> 11m 12m gb_12
> 12m 13m gb_17
> [ angles ]
> ; ai aj ak gromos type
> 1m 2m 3m ga_29
> 1m 2m 4m ga_18
> 3m 2m 4m ga_32
> 2m 4m 5m ga_31
> 2m 4m 6m ga_30
> 5m 4m 6m ga_17
> 4m 6m 7m ga_12
> 6m 7m 8m ga_14
> 7m 8m 19m ga_36
> 8m 19m 17m ga_6
> 19m 17m 18m ga_35
> 19m 17m 16m ga_6
> 19m 8m 9m ga_6
> 8m 9m 16m ga_6
> 9m 16m 17m ga_6
> 17m 16m 15m ga_38
> 8m 9m 10m ga_38
> 16m 9m 10m ga_26
> 9m 10m 11m ga_26
> 10m 11m 14m ga_26
> 11m 14m 15m ga_26
> 14m 15m 16m ga_26
> 15m 16m 9m ga_26
> 10m 11m 12m ga_18
> 11m 12m 13m ga_11
> 14m 11m 12m ga_18
> [ impropers ]
> ; ai aj ak al gromos type
> 2m 1m 4m 3m gi_1
> 4m 2m 5m 6m gi_1
> 8m 19m 9m 7m gi_1
> 9m 8m 16m 10m gi_1
> 11m 14m 12m 10m gi_1
> 16m 9m 15m 17m gi_1
> 17m 16m 18m 19m gi_1
> 8m 9m 16m 17m gi_1
> 9m 16m 17m 19m gi_1
> 16m 17m 19m 8m gi_1
> 17m 19m 8m 9m gi_1
> 19m 8m 9m 16m gi_1
> 9m 10m 11m 14m gi_1
> 10m 11m 14m 15m gi_1
> 11m 14m 15m 16m gi_1
> 14m 15m 16m 9m gi_1
> 15m 16m 9m 10m gi_1
> 16m 9m 10m 11m gi_1
> [ dihedrals ]
> ; ai aj ak al gromos type
> 1m 2m 4m 6m gd_4
> 7m 6m 4m 2m gd_19
> 8m 7m 6m 4m gd_17
> 19m 8m 7m 6m gd_20
> 10m 11m 12m 13m gd_2
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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