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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Received on Mon Jul 27 2015 - 11:00:02 PDT
