It really depends on how you want to use the files. Normally I prefer not
to change atom order and just change internal coordinates. It also depends
on the specific molecule, for example rings are much more complex. Changing
the dihedrals often works. Knowing which to change, and to what values, is
much easier with an understanding of internal coordinates. If you are
getting results that make sense, that's good. These changes affect only the
initial structure {as long as you preserve the connectivity and atom
types).
On Jul 27, 2015 1:37 PM, "Nicholus Bhattacharjee" <
nicholusbhattacharjee.gmail.com> wrote:
> Thanks for the reply. I need leap to build the coordinates. I just read (in
> amber forum) that if you change the sign of angle and dihedral column of
> the prep file you get prep file for the other enentiomer. I tried this and
> it worked although I don't know is it correct way. However, I am still in
> dilema how in the first place just interchanging one dihedral angle worked.
>
> On Mon, Jul 27, 2015 at 7:07 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > Yes you can use the prmtop for either chiral isomer. However that is not
> > the same as making a prep file. The prep file specifies both connectivity
> > and internal coordinates. If you want to change this for another isomer,
> > you need to leave the connectivity but change the internal coordinates.
> > However, this is not needed un less you need to use leap to build
> > coordinates. You haven't said why you need an alternate prep file so I'm
> > not sure what to suggest.
> > On Jul 27, 2015 12:52 PM, "Nicholus Bhattacharjee" <
> > nicholusbhattacharjee.gmail.com> wrote:
> >
> > > Hello,
> > >
> > > I am trying to generate prep file of a molecule which has a chiral
> > center.
> > > Let the chiral carbon be X and four atoms attached to them are 1, 2, 3
> > and
> > > 4. all of these atoms are also has sidechains. Now after preparing the
> R
> > > conformation prep file for the molcule I just interchanged the dihedral
> > > angle collumn of the 2 and 3 atom. I could generate the topology, crd
> and
> > > pdb files. Loading them with VMD shows different chirality for both of
> > > them. However, interestingly, I can load pdb file of one using topology
> > > file of another. Is that fine. I read about D amino acid in the amber
> > forum
> > > and it says that you only need to give the coordinate of D amino acid
> and
> > > it loads with the topology of L amino acid provided. Now considering
> > this I
> > > tried to make a prep file for D leucine by just interchanging the
> > dihedral
> > > column of HA and CB as shown below (I call it Deucine and DEU)
> > >
> > > DEUCINE
> > >
> > > DEU INT 1
> > > CORRECT OMIT DU BEG
> > > 0.00000
> > > 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.000
> > > 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.000
> > > 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.000
> > > 4 N n M 3 2 1 1.335 116.600 180.000 -.4937
> > > 5 H h E 4 3 2 1.010 119.800 0.000 .3018
> > > 6 CA c3 E 4 3 2 1.449 121.900 180.000 -.0097
> > > 7 HA h1 E 6 4 3 1.090 109.500 60.000 .0432
> > > 8 CB c3 3 6 4 3 1.525 111.100 300.000 -.1322
> > > 9 HB2 hc E 8 6 4 1.090 109.500 300.000 .0317
> > > 10 HB3 hc E 8 6 4 1.090 109.500 60.000 .0317
> > > 11 CG c3 3 8 6 4 1.525 109.470 180.000 .4429
> > > 12 HG hc E 11 8 6 1.090 109.500 300.000 -.0662
> > > 13 CD1 c3 3 11 8 6 1.525 109.470 60.000 -.4312
> > > 14 HD11 hc E 13 11 8 1.090 109.500 60.000 .1042
> > > 15 HD12 hc E 13 11 8 1.090 109.500 180.000 .1042
> > > 16 HD13 hc E 13 11 8 1.090 109.500 300.000 .1042
> > > 17 CD2 c3 3 11 8 6 1.525 109.470 180.000 -.4312
> > > 18 HD21 hc E 17 11 8 1.090 109.500 60.000 .1042
> > > 19 HD22 hc E 17 11 8 1.090 109.500 180.000 .1042
> > > 20 HD23 hc E 17 11 8 1.090 109.500 300.000 .1042
> > > 21 C c M 6 4 3 1.522 111.100 180.000 .6731
> > > 22 O o E 21 6 4 1.229 120.500 0.000 -.5854
> > >
> > >
> > > LOOP
> > >
> > >
> > > IMPROPER
> > > -M CA N H
> > > CA +M C O
> > >
> > > DONE
> > > STOP
> > >
> > >
> > > However it is not loading with loadamberprep. Considering the similar
> > idea
> > > in case of my molecule it should have loaded. I don't know the mistake
> I
> > am
> > > doing. However, both my R and S configuration of the molecule I created
> > > giving correct geometry. Thank you in advance for the suggestion.
> > > _______________________________________________
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> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> >
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Received on Mon Jul 27 2015 - 11:00:02 PDT
