AMBER Archive (2006)

Subject: RE: AMBER: Charges on atoms in protein :AMBER

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Feb 01 2006 - 22:17:24 CST

Dear Varsha,

Take a look at the CHARGE section of the prmtop file and see if there are
lots of atoms with zero charge. I doubt this is the problem though, the
charge on the TIP3P waters is defined in the library file used by leap.
Similarly the library files you loaded for HIC etc should contain charges.

More likely leap just doesn't write the charges to the pdb file, I assume
this is what you are loading into Sybyl, not the prmtop and inpcrd file.

Try creating a pdb file that includes the charges using ambpdb

ambpdb -pqr prmtop < inpcrd > pdb

Then take a look at it again in Sybyl.

All the best
Ross

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Varsha Goyal
> Sent: Wednesday, February 01, 2006 19:00
> To: amber_at_scripps.edu
> Subject: AMBER: Charges on atoms in protein :AMBER
>
> Hello,
> I generated pdb file after runnig leap:
>
> My leap.in is
>
> source leaprc.gaff
> source leaprc.ff99
> loadoff ZNC.lib
> loadoff HIC.lib
> loadoff HIF.lib
> loadoff wat.lib
> loadAmberParams frcmod.caii
> loadAmberParams frcmod.znc
> loadAmberParams ligand.frcmod
> loadAmberprep HIC.in
> loadAmberprep wat.in
> loadAmberprep ligand.prepin
> loadAmberprep HIF.in
> set BZO restype protein
> set ZNC restype protein
> set HIC restype protein
> set HIF restype protein
> Prot = loadPdb protein.pdb
> charge Prot
> addions Prot K+ 1
> solvateBox Prot TIP3PBOX 12 iso
> saveAmberParm Prot prmtop.top prmcrd.crd
> savepdb Prot protein-mod.pdb
> check Prot
> charge Prot
>
>
> But when i look at structure in Sybyl7.1 and try to
> display charge on residues i see 0.0 charge on every
> single atom. Does amber assign charge by itself or do
> we assign charges to residues before running leap.
>
> Thanks in advance,
> Varsha Gupta
>
>
>
>
>
>
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