[gmx-users] Error gmx pdb2gro
daniloboskovic0095 at gmail.com
Fri Jun 21 14:31:15 CEST 2019
Edit3: it contains TER and END lines (ffs finally).
On Fri, 21 Jun 2019, 14:30 Danilo Boskovic, <daniloboskovic0095 at gmail.com>
> Edit2: TER and END lines. Sorry for autocorrect.
> On Fri, 21 Jun 2019, 14:29 Danilo Boskovic, <daniloboskovic0095 at gmail.com>
>> 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>
>>> 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
>>> ATOM 2 O5' U B 501 24.120 9.582 -6.276 1.00 5.15
>>> ATOM 3 C4' U B 501 24.186 7.735 -4.679 1.00 4.12
>>> 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:
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