[gmx-users] fatal error

[Justin Lemkul]

On 3/6/17 10:23 AM, Urszula Uciechowska wrote:
>
> 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?
>

Did you check the .rtp for DC5, as Mark suggested?  Based on your knowledge of 
DNA structure, why might there be an issue with a 5'-phosphorus atom?

-Justin

> 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
>>>
>>>
>>>
>>>
>>> -----------------------------------------
>>> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
>>> http://www.ug.edu.pl/
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
>> a mail to gmx-users-request at gromacs.org.
>
>
>
> --------------------------------------------
> 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/
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================