On 4/01/2012 4:57 PM, Robert Hamers wrote:
I'd appreciate any help --
I'm trying to model a small (~ 20-carbon ) molecule linked to a
diamond surface. I got the diamond surface with >1500 atoms working
fine all the way through to the MD simulation and it looks great. But
I'm getting stuck on the molecule, which is not a protein but a
moderately short-chain molecule that has a triazole (N3C2) in the
middle of it. I thought in order to make this work I would need ot
learn how to with non-standard residues and after reading through the
manual endless times and searching on the web site and trying things
I'm basically stuck.
I thought it would easiest to deal with the triazole ring by creating
it as a non-standard residue in aminoacids.n2t. As a starting point I
thought I would try to work slowly by modifying an existing residue,
so I arbitrary decided to modify "alanine" in order to understand how
to work toward the more complicated triazole ring. So, in
atomtypebyname.atp I copied the entry for ALA and called it ZZZ, and
added a new entry "ZZZ Protein" into "residuetypes.dat". At that
point I can read in a pdb file with atoms belonging to residue "ZZZ"
and pdb2gmx works fine. However, if I try to change one of the
carbon atoms
to a nitrogen, (say, chance CA to N or NA), I get errors (see below)
that I'm having trouble interpreting. I thought that perhaps it was a
problem of having two atoms with the same definition, so I made one
"N1" and one "N2" as below, and also tried other variations (e.g., NA1
and NA2)
Atom naming needs to be unique within the residue, so that grompp can
later confirm that the order of the names in the topology and coordinate
files match.
(This is my entry in aminoacids.n2t)
aminoacids.rtp I assume you mean.
[ ZZZ ]
[ atoms ]
N1 opls_238 -0.500 1
H opls_241 0.300 1
N2 opls_238 0.140 1
HA opls_140 0.060 1
CB opls_135 -0.180 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
HB3 opls_140 0.060 2
C opls_235 0.500 3
O opls_236 -0.500 3
[ bonds ]
N1 H
N1 N2
N2 HA
N2 CB
N2 C
CB HB1
CB HB2
CB HB3
C O
-C N1
[ impropers ]
-C N2 N1 H improper_Z_N_X_Y
N2 +N1 C O improper_O_C_X_Y
I thought that this would lead to a structure that would connect "C"
to the previous residue in my pdb file and the "N" to the next .
However, when I do pdb2gmx, I get:
*N2* to the next, but yeah...
**
Back Off! I just backed up topol.top to ./#topol.top.40#
Processing chain 1 (13 atoms, 1 residues)
There are 0 donors and 1 acceptors
There are 0 hydrogen bonds
Identified residue ZZZ1 as a starting terminus.
Identified residue ZZZ1 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus ZZZ-1: NH3+
End terminus ZZZ-1: COO-
So the default(?) terminus selection is trying to give you charged
termini (perhaps because the type is protein, but I'm not sure here). It
is always appropriate to supply the command line you used.
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.3
Source code file: /build/buildd/gromacs-4.5.3/src/kernel/pdb2top.c,
line: 1056
Fatal error:
atom N not found in buiding block 1ZZZ while combining tdb and rtp
aminoacids.n.tdb applies to protein residues and assumes that NH3+ can
be applied. Evidently that won't work for your case. You will need to
come up with some termini that make sense, or use more than one residue.
************
I'm using the oplsaa force field, but up to this point it was a pretty
arbitrary decision.
I think my problem is understanding the mapping between atom names (
N1, HB1, etc) and the opls names, as I haven't yet found a good
explanation for how this mapping is done and/or what flexibility one
has in creating atom names for non-standard residues. (So, am I
allowed to create a N atom and call it N1, as long as I assign it to
an existing opls_xxx number ?) .
Yes. Atom and residue names exist only for matching pieces of force
fields together. The atom type determines the physics of the resulting
model. The two are technically orthogonal, but in practice there are
strong correlations.
Mark
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