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From: Nicholus Bhattacharjee <nicholusbhattacharjee.gmail.com>

Date: Mon, 27 Jul 2015 19:37:14 +0200

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.
*

*> > _______________________________________________
*

*> > AMBER mailing list
*

*> > AMBER.ambermd.org
*

*> > http://lists.ambermd.org/mailman/listinfo/amber
*

*> >
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

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

Date: Mon, 27 Jul 2015 19:37:14 +0200

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:

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

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