[gmx-users] Error in ligand coordinate file
Justin Lemkul
jalemkul at vt.edu
Wed Aug 8 12:08:01 CEST 2012
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
========================================
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