[gmx-users] Error in ligand coordinate file

[Justin Lemkul]

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

-- 
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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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