[gmx-users] RENUMTOP
Martina Bertsch, PhD
mbe404 at lulu.it.northwestern.edu
Sun Feb 15 08:13:00 CET 2004
Hi, David.
>>
>>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:
>>...
>>
>why? is there a covalent bond between your ligand and protein? otherwise
>this is not necessary at all.
>
I used 'renumtop' because when I just put an #include lig_vac.itp
statement after the #include ffG43b1 line in the top file (made by the
pdb2gmx for the protein), I got the warning from grompp that "the
topology is not renumbered from 1". I have never seen this message
before, but I remembered Anton mentioning 'renumtop', so I thought that
was somehow specific to ffG43a1/b1.
>>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".
>>
>Doesn'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.
>
No, there is no line number in the error message.
My ligand resembles tryptophan a little bit, so I borrowed some ffG43a1
parameters for Trp. I will try minimizing the ligand itself. But, is
there anything wrong with the format of my lig_vac.itp?
>>
>>
>>
>>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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