[gmx-users] Error gmx pdb2gro

[Justin Lemkul]

On 6/21/19 6:35 PM, Danilo Boskovic 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.

Use the -ter option and choose appropriate termini (5TER and 3TER for 
nucleic acids).

-Justin

> 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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-- 
==================================================

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

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