I'll respond to what I can.
On Jul 26, 2011, at 5:11 PM, Peter Varnai <P.Varnai.sussex.ac.uk> wrote:
> Hello,
>
> I prepare a protein prmtop file using tleap with current bug-fixed AmberTools15.
> I obtain different results using the commands below:
What are "results"?
>
> source leaprc.ff10
> prot = loadPdb prot.pdb
> saveAmberParm prot prot.top prot.crd
>
> or
>
> source leaprc.ff99SB
> prot = loadPdb prot.pdb
> saveAmberParm prot prot.top prot.crd
>
> I understand that the CA is now CX rather than CT but it should not change bonded force constants and equilibrium values?
No it shouldn't. According to my tests done prior to AmberTools 1.5 release, the prmtops for typical proteins (using typical amino acids) are different, but the results using sander or pmemd are identical.
>
> In case of using the ildn modifications with 'source leaprc.ff10' would give very different prmtop but:
>
> source leaprc.ff99SB
> loadamberparams frcmod.ff99SBildn
> loadOff all_amino94ildn.lib
> loadOff all_aminoct94ildn.lib
> loadOff all_aminont94ildn.lib
>
> or
>
> source leaprc.ff99SBildn
This is the "proper" way to load this force field.
>
> give almost the same prmtop except the modified Bondi radii - I wonder where these radii are stored for leap and why the new ildn atom types changed those.
These are stored in the leap source code. I forget where off the top of my head, but it's easily enough greppable. Assignments are done based on atom type and bonded neighbors (see the source code for details).
I've written a program that will (among other prmtop modifications) allow you to adjust the radii to whichever set you want. The logic leap uses to assign radii can be found in that source as well, which I can share with you if you want (it may be easier to read the logic in python with separate cases for each radii set rather than in C all jumbled together).
>
> I note that I do not see the latest OL modifications for RNA in ff10 in contrast to what is in the manual.
What's the "latest"? Some chi-mods in addition to the bcn parameters are found in parm10.dat itself, rather than in individual frcmod files. Hopefully a guru can expand on this.
HTH,
Jason
>
> Any insight would be appreaciated.
>
> Peter
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jul 26 2011 - 17:00:03 PDT
