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--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
