[gmx-users] Error in ligand coordinate file

sai nitin sainitin7 at gmail.com
Wed Aug 8 11:37:22 CEST 2012


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.

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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-- 

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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