[gmx-users] Atom types for phosphate group in OPLS-AA force field

Delmotte, Antoine antoine.delmotte09 at imperial.ac.uk
Thu Apr 26 17:37:40 CEST 2012


Dear Justin,

Many thanks for your response. I managed to reduce the number of errors 
by trying other atom types, by looking at what seemed most likely to be 
right from the ffnonbonded.itp and ffbonded.itp files.

Unfortunately, I did not manage to find a combination that both made 
some sense, and allowed to remove the errors. So I guess these things 
need to be parametrized, as you said.

Could you possibly let me know if there is a relatively easy and 
straightforward way to find these parameters? (I guess the answer is 
probably "no", but it's always worth asking, I guess...)

I also noticed that there is a option "-zero" in grompp which "Sets 
parameters for bonded interactions without defaults to zero instead of 
generating an error".

What does it mean exactly? Is it just taking the angles and distances 
inferred from the structure as the ones at equilibrium? Is it safe to 
use it?

I am just a beginner with MD, and I just want to do a quick run to test 
something. I have no need for super high accuracy, and the run I want to 
try will be very small (maybe 1 or 2 ns, or something like that), and 
for a very large system (~80 000 atoms). Would that be unreasonable to 
use that "-zero" option (it is tempting, I must say...)?

Thanks,

Antoine


On 26/04/12 12:53, Justin A. Lemkul wrote:
>
>
> On 4/26/12 7:45 AM, Delmotte, Antoine wrote:
>> Dear Gromacs users,
>>
>>
>> I am here requesting your help with regards to the editing of the 
>> OPLS-AA force
>> field, and more specifically, the choice of the atom types.
>>
>> I have added an entry for the molecule CABP to the .rtp and .hdb files.
>>
>> I can run pdb2gmx, genbox and editconf without getting any error. 
>> However, when
>> I run grompp, I receive the following errors:
>>
>> ERROR 1 [file 1RBO_Protein_chain_A.itp, line 15054]:
>> No default Bond types
>>
>> ERROR 78 [file 1RBO_Protein_chain_M.itp, line 47276]:
>> No default Angle types
>>
>> ERROR 82 [file 1RBO_Protein_chain_M.itp, line 66639]:
>> No default Ryckaert-Bell. types
>>
>> (there are 160 of those).
>>
>>
>>  From what I could see in this mailing list, it seems the error comes 
>> from the
>> choice of the atom types for the phosphate groups. I have tried 
>> several of them
>> which seemed to make sense, but none of them allowed to remove all 
>> the errors.
>>
>> The end of the chain is something like:
>>
>> O
>> |
>> (...)--CH2--O--P--O--H
>> |
>> O
>>
>> (details of the whole molecule here:
>> http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CAP&sid=1RBO
>> <http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CAP&sid=1RBO> )
>>
>> The problem is about the atom type of the -OH group at the end. Here 
>> are the
>> entries from the .atp file which I thought were relevant:
>>
>> opls_445 30.97376 ; P in MeOPO3--, MeOPO3H2
>> opls_446 15.99940 ; O= in MeOPO3--, MeOPO3H2
>> opls_447 15.99940 ; OMe in MeOPO3--, MeOPO3H2 methyl phosphate
>> opls_448 12.01100 ; C in MeOPO3--, MeOPO3H2 6-31+G* CHELPG
>> opls_449 1.00800 ; H in MeOPO3--, MeOPO3H2
>>
>> I chose opls_445 for the P, opls_446 for the 3 oxygens, and opls_449 
>> for the
>> hydrogen. Apparently, I got it wrong for the oxygen and the hydrogen 
>> of the OH
>> group, at least. Unless the error actually comes from something else...
>>
>> So my question is the following: Have I done something wrong about 
>> the atom
>> types? If so, does anyone know which atom type I should choose?
>>
>
> The problem isn't necessarily the atom types themselves (which seem to 
> be reasonable enough from the information provided), but rather that 
> there are no default bonded parameters for these interactions.  If you 
> look into ffnonbonded.itp, the second column is entitled "bond_type" 
> and thus refers to the names used by grompp when interpreting how 
> atoms are connected.  The actual bond, angle, and dihedral parameters 
> are in ffbonded.itp, using these names. You would have to map out what 
> the bond_type names are for each of these and find/derive new 
> parameters for each of the interactions that are missing.
>
> -Justin
>
>> Details of my rtp entry:
>>
>> [ CAP ]
>> [ atoms ]
>> P1 opls_445 1.539429 1
>> O1P opls_446 −0.818751 1
>> O2P opls_446 −0.899293 1
>> HO2P opls_449 0.429028 1
>> O3P opls_446 −0.895147 1
>> O1 opls_447 −0.772438 2
>> C1 opls_448 0.022084 3
>> HC11 opls_449 0.176920 3
>> HC12 opls_449 0.139342 3
>> C2 opls_159 0.146383 4
>> O2 opls_154 −0.883774 4
>> HO2 opls_155 0.527657 4
>> C opls_271 0.815849 5
>> O6 opls_271 −0.766517 5
>> O7 opls_272 −0.771422 5
>> C3 opls_158 0.142583 6
>> HC3 opls_140 0.107158 6
>> O3 opls_154 −0.817159 6
>> HO3 opls_155 0.471262 6
>> C4 opls_158 0.184473 7
>> HC4 opls_140 0.164192 7
>> O4 opls_154 −0.822792 7
>> HO4 opls_155 0.498509 7
>> C5 opls_448 0.038563 8
>> HC51 opls_449 0.143027 8
>> HC52 opls_449 0.135804 8
>> O5 opls_447 −0.730025 9
>> P2 opls_445 1.526672 10
>> O4P opls_446 −0.866625 10
>> O5P opls_446 −0.810148 10
>> HO5P opls_449 0.521464 10
>> O6P opls_446 −0.876311 10
>> [ bonds ]
>> HO2P O2P
>> O1P P1
>> O2P P2
>> O3P P1
>> P1 O1
>> O1 C1
>> C1 HC11
>> C1 HC12
>> C1 C2
>> C2 O2
>> O2 HO2
>> C2 C
>> C O6
>> C O7
>> C2 C3
>> C3 O3
>> C3 HC3
>> O3 HO3
>> C3 C4
>> C4 HC4
>> C4 O4
>> O4 HO4
>> C4 C5
>> C5 HC51
>> C5 HC52
>> C5 O5
>> O5 P2
>> P2 O4P
>> P2 O5P
>> P2 O6P
>> O5P HO5P
>>
>> Thank you very much in advance!
>>
>> Antoine
>>
>>
>



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