[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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