[gmx-users] Help with non-standard residues and molecular structures
rjhamers at wisc.edu
Wed Jan 4 18:33:27 CET 2012
Thanks-- that clarifies a lot. I hadn't quite realized how much is
assumed about the residue terminii. It seems like I was trying to fit a
square peg into a round hole. I'm going to re-think this and maybe
take a different approach just based on using HETATMs and not trying to
define a separate residue.
The pdb file specification for HETATM still requires a "residue name".
I've found that using "LIG" seems to work. Any reason I shouldn't just
continue using that, and define my molecule using HETATMs ?
Thanks again for your help!
For something like what I'm trying to do, where I"m using a pdb file
that does not represent a protein, is
On 1/4/2012 2:02 AM, Mark Abraham wrote:
> 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.
Robert J. Hamers
Wisconsin Distinguished Professor
Univ. of Wisconsin-Madison
1101 University Avenue
Madison, WI 53706
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