[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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