[gmx-users] pdb2gmx
Justin Lemkul
jalemkul at vt.edu
Wed Jun 5 03:16:09 CEST 2013
On 6/4/13 12:05 PM, Valentina Erastova wrote:
> Hello all,
>
> I am converting a .pdb into .gro and .top and assigning ClayFF forcefield, that is not included in the gromacs.
>
> It's a strange FF as doesn't have ones between all of the atoms, just O-H but it has an angle between a metal and OH, therefore I wore out molecule.rtp (see below) that included the angles, BUT wen I convert to the .top I only get bonds, but not angles (see below). Is there something I am missing or does gromacs not assign angles if no bonds are assigned?
>
That's probably correct, given that normally pdb2gmx will build angles based on
bonds that are present. Most "normal" usage will never have angles without
bonds, so for now, you will have to write the angles in the topology yourself.
I will file a bug report with a (much simpler) test case so we don't lose track
of this issue. Given that it affects so few simulations, it may be a while
before it is resolved, but it may well be worth doing simply for flexibility
reasons.
-Justin
> Thank you!
>
>
>
> molecule.rtp
> [ B31 ] ;# ldh21
> [ atoms ]
> ; atomname atomtype charge chargegroup
> ; charges were taken from paper by Kuang Wu and J R Schmidt; J Phys Chem C (2012)
> ; and edited to make it fir LDH31 model and produce +1
> o1 ohs -1.113 0
> h1 ho 0.464 0
> o2 ohs -1.113 0
> h2 ho 0.464 0
> o3 ohs -1.113 0
> h3 ho 0.464 0
> o4 ohs -1.113 0
> h4 ho 0.464 0
> mg1 mgo 1.403 0
> al1 ao 1.983 0
> o5 ohs -1.113 0
> h5 ho 0.464 0
> o6 ohs -1.113 0
> h6 ho 0.464 0
> o7 ohs -1.113 0
> h7 ho 0.464 0
> o8 ohs -1.113 0
> h8 ho 0.464 0
> mg2 mgo 1.403 0
> mg3 mgo 1.403 0
> [ bonds ]
> ; atom1 atom2 parametersindex
> o1 h1 ohs
> o2 h2 ohs
> o3 h3 ohs
> o4 h4 ohs
> o5 h5 ohs
> o6 h6 ohs
> o7 h7 ohs
> o8 h8 ohs
> [ angles ]
> ; ai aj ak gromos type
> mg1 o1 h1 moh
> mg1 o8 h8 moh
> mg1 o4 h4 moh
> mg1 o6 h6 moh
> mg1 o3 h3 moh
> mg1 o5 h5 moh
> al1 o3 h3 moh
> al1 o5 h5 moh
> al1 o2 h2 moh
> al1 o7 h7 moh
> al1 o4 h4 moh
> al1 o6 h6 moh
> mg2 o8 h8 moh
> mg2 o2 h2 moh
> mg2 o5 h5 moh
> mg2 o4 h4 moh
> mg2 o7 h7 moh
> mg2 o1 h1 moh
> mg3 o7 h7 moh
> mg3 o1 h1 moh
> mg3 o6 h6 moh
> mg3 o3 h3 moh
> mg3 o8 h8 moh
> mg3 o2 h2 moh
>
>
>
> ldh31.top
> ; Include forcefield parameters
> #include "./ClayFF.ff/forcefield.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> Other 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
> ; residue 1 B31 rtp B31 q +1.0
> 1 ohs 1 B31 o1 1 -1.113 16 ; qtot -1.113
> 2 ho 1 B31 h1 1 0.464 1.008 ; qtot -0.649
> 3 ohs 1 B31 o2 1 -1.113 16 ; qtot -1.762
> 4 ho 1 B31 h2 1 0.464 1.008 ; qtot -1.298
> 5 ohs 1 B31 o3 1 -1.113 16 ; qtot -2.411
> 6 ho 1 B31 h3 1 0.464 1.008 ; qtot -1.947
> 7 ohs 1 B31 o4 1 -1.113 16 ; qtot -3.06
> 8 ho 1 B31 h4 1 0.464 1.008 ; qtot -2.596
> 9 mgo 1 B31 mg1 1 1.403 24.31 ; qtot -1.193
> 10 ao 1 B31 al1 1 1.983 26.98 ; qtot 0.79
> 11 ohs 1 B31 o5 1 -1.113 16 ; qtot -0.323
> 12 ho 1 B31 h5 1 0.464 1.008 ; qtot 0.141
> 13 ohs 1 B31 o6 1 -1.113 16 ; qtot -0.972
> 14 ho 1 B31 h6 1 0.464 1.008 ; qtot -0.508
> 15 ohs 1 B31 o7 1 -1.113 16 ; qtot -1.621
> 16 ho 1 B31 h7 1 0.464 1.008 ; qtot -1.157
> 17 ohs 1 B31 o8 1 -1.113 16 ; qtot -2.27
> 18 ho 1 B31 h8 1 0.464 1.008 ; qtot -1.806
> 19 mgo 1 B31 mg2 1 1.403 24.31 ; qtot -0.403
> 20 mgo 1 B31 mg3 1 1.403 24.31 ; qtot 1
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 1 ohs
> 3 4 1 ohs
> 5 6 1 ohs
> 7 8 1 ohs
> 11 12 1 ohs
> 13 14 1 ohs
> 15 16 1 ohs
> 17 18 1 ohs
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> [ system ]
> ; Name
> God Rules Over Mankind, Animals, Cosmos and Such
>
> [ molecules ]
> ; Compound #mols
> Other 1--
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--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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