[gmx-users] Error gmx pdb2gro

[Danilo Boskovic]

Edit3: it contains TER and END lines (ffs finally).

On Fri, 21 Jun 2019, 14:30 Danilo Boskovic, <daniloboskovic0095 at gmail.com>
wrote:

> Edit2: TER and END lines. Sorry for autocorrect.
>
> On Fri, 21 Jun 2019, 14:29 Danilo Boskovic, <daniloboskovic0095 at gmail.com>
> wrote:
>
>> Edit: the structure is a split_chain generated and exported file from
>> pymol. It contains only the structure coordinates in format as stated
>> above, so please TER and END.
>>
>> On Fri, 21 Jun 2019, 14:14 Danilo Boskovic, <daniloboskovic0095 at gmail.com>
>> wrote:
>>
>>> I am trying to backmap an RNA file from the MARTINI tutorial as stated
>>> in the tutorial but i am getting error atom N not found in buiding block
>>> while combining tdb and rtp when trying to generate a topology file. Im
>>> using Gromacs 2018.7. It also says
>>>
>>> Start terminus U-501: NH3+
>>> End terminus A-511: COO-
>>>
>>> for an RNA.
>>>
>>> Example first three lines of PDB file:
>>>
>>> ATOM      1  C5'   U B 501      23.332   8.576  -5.633  1.00  4.88
>>>     C
>>> ATOM      2  O5'   U B 501      24.120   9.582  -6.276  1.00  5.15
>>>     O
>>> ATOM      3  C4'   U B 501      24.186   7.735  -4.679  1.00  4.12
>>>     C
>>>
>>> It seems that the format of the PDB is recognized as a protein. I am
>>> using CHARMM and tip3p. I have a tip3p.itp file, tried to use #include but
>>> it did not help. For full tutorial:
>>>
>>> http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/tutorial-martini-rna-gmx5
>>>
>>>