This looks very strange that from the whole assortment of the molecules
in the force field only a humble methyl group in thymine lacks proper
definition causes such an error.
Even nucleotides which I added myself to the force field files don't
produce any errors
Is there any way to remedy this without significant hassle? What things
are exactly lacking?
------------------------------
Message: 4
Date: Thu, 8 Oct 2015 11:15:17 +0000
From: Erik Marklund <erik.markl...@chem.ox.ac.uk>
To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
Subject: Re: [gmx-users] Virtual sites error
Message-ID: <89ae0bec-6d9f-49a0-83e2-5ad8d7734...@chem.ox.ac.uk>
Content-Type: text/plain; charset="us-ascii"
Unfortunately, the parameters required for certain virtual sites in nucleic
acids are not define in the force field files that are shipped with Gromacs.
Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College
Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ
On 7 Oct 2015, at 11:33, Timofey Tyugashev <tyugas...@niboch.nsc.ru> wrote:
Trying to add hydrogen virtual sites to the model (using -vsites h option in
pdb2gmx) results in a salvo of error messages when running grommp to create
.tpr file after the solvation:
ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]:
No default Constr. No Conn. types
ERROR 2 [file topol_DNA_chain_A2.itp, line 1034]:
No default Constr. No Conn. types
This lines in constraints section in the .itp file refer to pairs of two MCH3
and one MC atoms, which should serve (the way I understand the situation) as
replacement methyl group in thymine. There are several more pairs of same
errors corresponding to different thymine methyl groups in the DNA strands.
Here is the relevant sections of the itp file for the first two errors:
[ constraints ]
; ai aj funct c0 c1
2 3 2
110 111 2
110 112 2
111 112 2
[ atoms ]
110 CM 321 DT C5 110 0.0025 12.01 ; qtot -2.867
111 MCH3 321 DT MC71 111 0 7.517 ; qtot -2.867
112 MCH3 321 DT MC72 111 0 7.517 ; qtot -2.867
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