[gmx-users] Error in ligand coordinate file
sai nitin
sainitin7 at gmail.com
Wed Aug 8 16:44:44 CEST 2012
Hi justin,
Ok i will explain more clearly what i really have is protein ligand
complex from Autodock..I choose best complex based on predicted
binding affinity. Using pymol i visualized complex.pdb and saved only
ligand (ligand.pdb given below) and used swiss param tool online
http://swissparam.ch/ to charmm 27 FF .itp file then i followed
tutorial and ran 10ns simulation now wanted to use g_lie to calculate
binding free energies..of this complex..so have to run one more
simulation for ligand only in water right...for that im using
coordinate file which i have saved it from pymol
in original PDB file it is properly aligned :)
ATOM 1 C <1> d 83.432 21.209 56.133 -0.07 -0.02 C
ATOM 2 C <1> d 84.828 21.291 56.786 -0.29 0.00 C
ATOM 3 O <1> d 83.629 21.200 54.697 -0.02 -0.07 O
ATOM 4 C <1> d 85.679 20.564 55.751 -0.19 -0.02 C
ATOM 5 C <1> d 85.046 21.032 54.436 -0.15 0.04 C
ATOM 6 N <1> d 82.546 22.305 56.532 -0.10 -0.05 N
ATOM 7 C <1> d 81.884 22.186 57.757 0.18 0.05 C
ATOM 8 N <1> d 81.028 23.185 58.155 0.01 -0.07 N
ATOM 9 O <1> d 82.069 21.213 58.493 -0.09 0.04 O
ATOM 10 C <1> d 80.868 24.232 57.405 -0.07 0.06 C
ATOM 11 C <1> d 81.567 24.413 56.119 -0.49 0.00 C
ATOM 12 C <1> d 82.377 23.424 55.745 -0.38 0.02 C
ATOM 13 N <1> d 80.012 25.195 57.842 0.39 0.02 N
ATOM 14 H <1> d 79.062 24.997 58.139 -0.05 -0.06 H
ATOM 15 H <1> d 80.312 26.164 57.884 -0.11 -0.01 H
ATOM 16 O <1> d 84.944 20.703 58.090 0.01 0.19 O
ATOM 17 H <1> d 85.311 19.798 57.956 -0.17 -0.58 H
ATOM 18 O <1> d 85.512 19.135 55.900 0.09 0.57 O
ATOM 19 H <1> d 84.884 19.014 56.648 -0.30 -0.75 H
ATOM 20 C <1> d 85.627 22.354 53.918 -0.22 0.11 C
ATOM 21 O <1> d 84.597 23.194 53.394 -0.56 -0.44 O
ATOM 22 H <1> d 83.757 22.697 53.521 0.27 0.18 H
END
Im running PDB2GMX to generate topol.top file..for this ligand by
CHARMM 27 FF but it gives following error
Fatal error:
Residue '<1>' not found in residue topology database
So now question how to solve this error..? Can you please suggest some help ?
thanks,
Nitin
On Wed, Aug 8, 2012 at 12:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 8/8/12 5:37 AM, sai nitin wrote:
>>
>> Hi justin,
>>
>> Thanks for reply now i have ligand corrdinate file as follows
>>
>> ATOM 1 N A -13.006 -12.965 -0.251 -0.60 -0.09 N
>> ATOM 2 C A -13.386 -13.020 1.035 -0.38 0.03 C
>> ATOM 3 C A -13.037 -14.131 1.869 -0.32 -0.03 C
>> ATOM 4 C A -12.284 -14.007 -0.761 -0.21 0.02 C
>> ATOM 5 N A -11.897 -15.079 0.059 -0.24 -0.01 N
>> ATOM 6 C A -12.288 -15.172 1.391 -0.37 0.01 C
>> ATOM 7 N A -13.547 -13.886 3.036 -0.34 0.14 N
>> ATOM 8 N A -14.076 -12.193 1.759 -0.27 0.01 N
>> ATOM 9 C A -14.163 -12.729 2.956 -0.29 -0.08 C
>> ATOM 10 N A -11.887 -13.919 -2.092 -0.05 0.04 N
>> ATOM 11 H A -11.305 -15.802 -0.326 -0.11 -0.03 H
>> ATOM 12 H A -12.027 -12.978 -2.454 -0.07 -0.16 H
>> ATOM 13 C A -11.368 -14.845 -3.008 -0.39 0.00 C
>> ATOM 14 C A -11.534 -14.731 -4.394 -0.49 0.00 C
>> ATOM 15 C A -11.032 -15.710 -5.270 -0.32 0.00 C
>> ATOM 16 C A -10.360 -16.822 -4.750 -0.24 0.00 C
>> ATOM 17 C A -10.189 -16.950 -3.375 -0.33 0.00 C
>> ATOM 18 C A -10.690 -15.970 -2.515 -0.42 0.00 C
>> ATOM 19 C A -11.203 -15.559 -6.724 -0.27 0.00 C
>> ATOM 20 C A -12.302 -15.958 -7.389 -0.19 0.02 C
>> ATOM 21 O A -11.918 -16.240 2.152 -0.14 -0.09 O
>> ATOM 22 H A -11.168 -16.702 1.710 -0.26 -0.13 H
>> END
>>
>> Still not working
>>
>> Fatal error:
>> Atom N in residue A 0 was not found in rtp entry RA with 32 atoms
>> while sorting atoms.
>>
>
> Your molecule has to correspond to some known entity in the force field.
> Here, with the residue name "A," the closest match pdb2gmx can find is to
> the ribonucleotide RA. If that's what this is, then your atom names need to
> match with what is expected.
>
> It also appears your columns are still misaligned.
>
> -Justin
>
>
>> Any help ??
>>
>> Thanks,
>> Nitin
>>
>> On Tue, Aug 7, 2012 at 11:42 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>
>>> On 8/7/12 5:08 AM, sai nitin wrote:
>>>>
>>>>
>>>> Hi all,
>>>>
>>>> Recently i performed protein ligand complex simulation my aim is to
>>>> compute free energy values using g_lie..i came across that to perform
>>>> g_lie analysis one should two 2 MD simulation one is protein ligand
>>>> complex simulation (this is done ) used Charmm 27 FF second one is
>>>> simulate ligand in water...which is the step i got stuck i know it is
>>>> simple but couldnt get through first step it self preparing ligand
>>>> coordinate file which i already have as follows i ran PDB2gmx to
>>>> generate topol.top file but couldnt succeed.. ligand coordinate file
>>>> is given below
>>>>
>>>> ATOM 1 N -13.006 -12.965 -0.251 1.00 0.00 N
>>>> ATOM 2 C -13.386 -13.020 1.035 1.00 0.00 C
>>>> ATOM 3 C1 -13.037 -14.131 1.869 1.00 0.00 C
>>>> ATOM 4 C2 -12.284 -14.007 -0.761 1.00 0.00 C
>>>> ATOM 5 N1 -11.897 -15.079 0.059 1.00 0.00 N
>>>> ATOM 6 C3 -12.288 -15.172 1.391 1.00 0.00 C
>>>> ATOM 7 N2 -13.547 -13.886 3.036 1.00 0.00 N
>>>> ATOM 8 N3 -14.076 -12.193 1.759 1.00 0.00 N
>>>> ATOM 9 C4 -14.163 -12.729 2.956 1.00 0.00 C
>>>> ATOM 10 N4 -11.887 -13.919 -2.092 1.00 0.00 N
>>>> ATOM 11 H -11.305 -15.802 -0.326 1.00 0.00 H
>>>> ATOM 12 H1 -12.027 -12.978 -2.454 1.00 0.00 H
>>>> ATOM 13 C5 -11.368 -14.845 -3.008 1.00 0.00 C
>>>> ATOM 14 C6 -11.534 -14.731 -4.394 1.00 0.00 C
>>>> ATOM 15 C7 -11.032 -15.710 -5.270 1.00 0.00 C
>>>> ATOM 16 C8 -10.360 -16.822 -4.750 1.00 0.00 C
>>>> ATOM 17 C9 -10.189 -16.950 -3.375 1.00 0.00 C
>>>> ATOM 18 C10 -10.690 -15.970 -2.515 1.00 0.00 C
>>>> ATOM 19 C11 -11.203 -15.559 -6.724 1.00 0.00 C
>>>> ATOM 20 C12 -12.302 -15.958 -7.389 1.00 0.00 C
>>>> ATOM 21 O -11.918 -16.240 2.152 1.00 0.00 O
>>>> ATOM 22 H2 -11.168 -16.702 1.710 1.00 0.00 H
>>>> ATOM 23 H3 -14.661 -12.289 3.746 1.00 0.00 H
>>>> ATOM 24 H4 -12.034 -13.914 -4.779 1.00 0.00 H
>>>> ATOM 25 H5 -9.992 -17.547 -5.386 1.00 0.00 H
>>>> ATOM 26 H6 -9.692 -17.769 -2.991 1.00 0.00 H
>>>> ATOM 27 H7 -10.559 -16.076 -1.497 1.00 0.00 H
>>>> ATOM 28 H8 -10.438 -15.123 -7.263 1.00 0.00 H
>>>> ATOM 29 H9 -13.084 -16.397 -6.878 1.00 0.00 H
>>>> ATOM 30 H10 -12.364 -15.825 -8.411 1.00 0.00 H
>>>>
>>>>
>>>> Running PDB2gmx gives error as follows
>>>>
>>>> Fatal error:
>>>> Residue '-13.' not found in residue topology database
>>>>
>>>>
>>>> Can any tell me what is wrong in my coordinate file ....
>>>>
>>>
>>> It is formatted incorrectly. PDB format requires fixed spacing and
>>> correct
>>> content. The file shown above lacks a residue name column.
>>>
>>> -Justin
>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>> --
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>>
>>
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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--
Sainitin D
PhD student
Bioinformatics Group
Biotechnology Center
Technische Universität Dresden
Tatzberg 47/49
01307 Dresden, Germany
Tel Lab:+49 (0)351 463 40060
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