[gmx-users] Error gmx pdb2gro

[Danilo Boskovic]

Bump..

On Sat, 22 Jun 2019, 00:35 Danilo Boskovic, <daniloboskovic0095 at gmail.com>
wrote:

> OK. And could you explain how? I just started to learn doing simulations
> and am an undergraduate. Can't find any documentation on what you said I
> need to do.
>
> On Fri, 21 Jun 2019, 16:11 Justin Lemkul, <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/21/19 8:14 AM, Danilo Boskovic 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
>>
>> You have to manually choose termini with CHARMM36. This is because there
>> is no way to split proteins, nucleic acids, etc. into their own files
>> automatically when reading in the whole force field and we try to avoid
>> hard-coding as much as we possibly can.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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>