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)
(This is my entry in aminoacids.n2t)
[ 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:
**
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-
-------------------------------------------------------
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
************
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 ?) .
Any suggestions would be very welcome....
Thanks!
Bob Hamers
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