On May 15 2012, case wrote:
>On Tue, May 15, 2012, C.M. Baker wrote:
>>
>> I'm running some simulations of DNA (canonical B-form) using amber with
>> the parmbsc0 parameter set. Everything seems to work fine, but I've
>> noticed that I get different results depending on whether I use tleap or
>> sleap for my initial system set-up.
>
>>
>> source leaprc.ff99bsc0
>> dna1 = loadPdb 1BNA_no_waters.pdb
>> saveAmberParm dna1 1bna_99.prmtop 1bna_99.prmcrd
>
>At this point, you could use readparm to print and examine the dihedral
>angle parameters (say esp. around delta) in the prmtop files created by
>tleap and sleap. Looking at energies of the initial coordinates should
>also show whether or not there are any differences that would eventually
>result in different distributions of angles.
>
> leaprc.ff99bsc0 reads in a main parameter file, followed by two frcmod
> files. This leads me to suspect that the differences may arise from how
> frcmod files are interpreted. One way to test this is to try sleap vs.
> tleap using leaprc.ff10, which does not make use of frcmod files. Again,
> I'd think that close examination of the prmtop files, or of single point
> energies, should suffice; one presumably doesn't need to run converged
> simulations from each option.
>
>....dac
>
Thanks for the quick reply. As you suggested, I've been running some single
point calculations, and looking at the resulting energies.
With parmbsc0, if I read in my DNA molecule and calculate a single point
energy (no ion, no solvent), I get exactly the same results regardless of
whether I use tleap or sleap.
However, if I add solvent then things change. Now if I do a single point
calculation, the angle energies are very different. And if I look at the
resulting prmtop files, is shows that there are number number of atom types
in each case:
tleap:
%FLAG POINTERS
%FORMAT(10I8)
12953 17 12467 544 640 836 1294 1520 0 0
20470 4089 544 836 1520 43 86 48 28 1
0 0 0 0 0 0 0 2 34 0
0
sleap:
%FLAG POINTERS
%FORMAT(10I8)
12953 16 12467 544 1280 1672 1294 1520 0 0
20470 4089 544 1672 1520 32 59 48 16 0
0 0 0 0 0 0 0 2 34 0
0
Looking at the "%FLAG ATOM_TYPE_INDEX" section of the prmtop files, the
first atom in the parameter file (HO) is given type 1. When I use sleap,
all of the water H atoms are also give type 1; when I use tleap, the water
H atoms are given type 17.
This seems a little strange, and like it might well result in differences
in simulations run with the resulting prmtop files. If you have any
thoughts on what is going on here, I would be grateful to hear them.
Thanks again for your help,
Chris
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Received on Wed May 16 2012 - 05:00:02 PDT
