[gmx-users] fatal error

[Urszula Uciechowska]

Hi,

I do not know. After running pdb2gmx I am not getting the .itp file for
the DC5... I am using gromacs 5.0.4. What can be wrong here?

Urszula

> Hi,
>
> What name does the .rtp entry for DC5 use for its phosphorus atom?
>
> Mark
>
> On Mon, Mar 6, 2017 at 1:39 PM Urszula Uciechowska <
> urszula.uciechowska at biotech.ug.edu.pl> wrote:
>
>> Dear gmx users,
>>
>> After running a pdb2gmx script of the pdb file I am getting an error
>> message:
>>
>>
>> Fatal error:
>> Atom P in residue DC 2 was not found in rtp entry DC5 with 28 atoms
>> while sorting atoms.
>>
>>
>> The DC 2 in pdb file:
>>
>> TER   11412      LEU B 366
>> ATOM  11413  P   DC  C   2       0.997  17.702   5.368  1.00 77.21
>>   P
>> ATOM  11414  OP1 DC  C   2      -0.278  17.623   4.612  1.00 76.82
>>   O
>> ATOM  11415  OP2 DC  C   2       1.374  16.596   6.287  1.00 76.77
>>   O
>> ATOM  11416  O5' DC  C   2       2.181  17.899   4.319  1.00 75.66
>>   O
>> ATOM  11417  C5' DC  C   2       2.302  19.107   3.565  1.00 72.46
>>   C
>>
>> What can be wrong with the P atom?
>>
>> Thanks for any suggestions.
>>
>> best
>> Urszula Uciechowska
>>
>>
>>
>>
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--------------------------------------------
Urszula Uciechowska PhD
University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Abrahama 58
80-307 Gdańsk
Poland


-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/