[Dock-fans] DOCK3.6 parameters for ion, DNA, and RNA, and question on pharmacophore matching

Trent E. Balius tbalius at aol.com
Fri Dec 12 14:51:18 PST 2014


Thanks.  I am forwarding this to the mailing list. 

 Trent

 

-----Original Message-----
From: Yi Shang <mirandaisbest at gmail.com>
To: Trent E. Balius <tbalius at aol.com>
Sent: Fri, Dec 12, 2014 2:47 pm
Subject: Re: [Dock-fans] DOCK3.6 parameters for ion, DNA, and RNA, and question on pharmacophore matching


I found out the charges were because you have some extra atoms defined beginning with A, like you have AD2 and AD1 atoms for ASN. When you ignore these atoms the charges are fine.




On Tue, Dec 9, 2014 at 4:48 PM, Yi Shang <mirandaisbest at gmail.com> wrote:

Hi Trent,
I was trying to map the polar H naming. And I sum up charges in prot.table.ambcrg.ambH for each amino acids:



ALA charge: -2.77556e-17
ARG charge: 1
ASN charge: -1.337
ASP charge: -1
CYS charge: 0
GLN charge: -1.337
GLU charge: -1
GLY charge: 0
HIS charge: 0.535

HIE charge: -0.465
HID charge: -0.442
HIP charge: 0.773

ILE charge: 0
LEU charge: -5.55112e-17
LYS charge: 1
MET charge: 0
PHE charge: 0
PRO charge: 0
SER charge: -5.55112e-17
THR charge: -5.55112e-17
TRP charge: 5.55112e-17
TYR charge: -5.55112e-17
VAL charge: 0



I am confused by the charges of histidine (different protonations), ASN, GLN, could you explain why HIE, HID, ASN, and GLN are not neutral?


Thank you!










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