[gmx-users] Error gmx pdb2gro
jalemkul at vt.edu
Fri Jun 28 19:12:46 CEST 2019
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
> 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
>>> 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
>>> CHARMM and tip3p. I have a tip3p.itp file, tried to use #include but it
>>> not help. For full tutorial:
>> 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 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
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Justin A. Lemkul, Ph.D.
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
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