Dear Shau,
> 1) My concern for using the first approach is that C1' atom bears a
> fairly
> large negative charge, and the nearby atoms of the modified base (close
> to C1') are also affected to some noticeable degree.
Yes it seems strange. When I applied this 1st startegy on my unusual nucleotide
I got similar charge values that those reported in table VI page 1368. I think
deriving RESP charges when you do it for the 1st time is quite tricky and error
prone. For instance, in this approach, C1 charges must be free; i.e. without
inter-molecular restraints (Are you sure you applied this ?)... We wrote RED
http://www.u-picardie.fr/labo/lbpd/RED/ to help people using RESP. You will find
tutorials but it is only for simple cases; i.e. there is no intermolecule
restraints. Anyway, you might found some information useful in the manual also.
> Secondly, if I were to use the
> RESP charges generated using the first approach, do I define a new
> residue in xleap for the modified nucleotide?
I would say you load the PDB file (it is obviously not recognized), you create
the bond (bondbydistance command), you enter 'manually' the RESP charges you
calculated and the atom types you selected (i.e you can "edit" the unit) and you
save the OFF library (.off file), coordinates (prmcrd) and topology/FF
information (prmtop). Try for instance this:
source leaprc.ff98
M = loadpdb Mol.pdb
# M is the 'unit' name, Mol.pdb is your PDB fike
bondbydistance M
edit M
# you enter manually the charges values
# and atom type in the table displayed
saveoff M M.off
# M.off can be loaded with 'loadoff M.off'
saveamberparm M prmtop prmcrd
It is done for 'in vacuo' simulation. But you might want to add ion and solvate
your system in a box of solvant...
source leaprc.ff98
M = loadpdb Mol.pdb
bondbydistance M
edit M => add charges and atom types...
solvateoct M WATBOX256 10
addions Na+ 0
saveoff M M.off
saveamberparm M prmtop prmcrd
Reday for, periodic simulations...
> 2) If I were to use the second approach as you mentioned with the
> restraint of .126
First I would use .1268 and not .126 that will help you to get a 'more neutral
system' and this might be problematic if you want to neutralize with ions in
leap...
>(during the second stage, I assume),
No it is in the 1st stage and after you freeze the charges in the second
stage...
>I
> would then assign these RESP charges to the base atoms in the PREP
> module
> as suggested in JACS, 119, 7095-7104). My question is that what charges
> I would use for C1' and H1' atoms in this case.
The strategy is different, in the Cieplak's paper the C1 is free because
inter-molecular restraints are used (allows the system to be more free, allows
to get a better fit between the electrostaic potential and the charges). In the
second approche, you do not use inter-molecular restraints because you unusual
base is rigid...
I hope that will help you. Regards, Francois
F.-Y. Dupradeau
--
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France
--
http://www.u-picardie.fr/labo/lbpd/fyd.htm
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Feb 20 2004 - 17:53:01 PST
