[gmx-users] Error gmx pdb2gro

[Danilo Boskovic]

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
>>
>>