Questions about user-modified forcefield files and about ligands

[Kenneth Cheng]

Dear APBS developers and users,

I'm not a professional computational biochemist and just seeking to adopt APBS to explore some problems in my research project. I've encountered barriers soon as I got started and couldn't find answers elsewhere, so I hope to get some help here. Thanks!

I'm working on a protein with manganese ion (MN) in its active site, as well as an acetylated lysine residue which comes as a unique residue named ALY. Nothing else is special with this protein. I suppose I have to add ALY to AA.xml, in addition to adding parameters for MN and ALY into the forcefield files, is this right? Is there anything else I should do before running pdb2pqr?

I'm using CHARMM forcefield, the .dat file goes like this:

1        2   3          4                5 

ALA   N   -0.47   1.850000   NH1

Could anybody explain Column 3 and 4, what they stand for and their units? So that I can try to find the desired parameters for my missing items.

Another problem is that I would like to generate a separate pqr file for a ligand molecule, the superoxide anion. I've generated its pdb file which goes like this:

COMPND    SUPEROXIDE ANION 

HET    SPO      1       2     SUPEROXIDE ANION

FORMUL    1  SPO    O2

ATOM      1  O   SPO     1      12.579  -7.067   0.000  1.00  0.00           O  

ATOM      2  O   SPO     1      14.278  -7.067   0.000  1.00  0.00           O

CONECT    1    2                                                      

CONECT    2    1                                                      

MASTER        0    0    0    0    0    0    0    0    2    0    2    0

END

I'd like to know what's to be done before I pass it to pdb2pqr to properly get a pqr file. Modify the forcefield? What else?

I would really appreciate your hints or guidance!

[Kenneth Cheng]

Dear all,

I've understood the format of the forcefield parameter file and added the parameters for ALY, MN and superoxide anion. Below are the lines I added to CHARMM.dat:

ALY    N -0.47 1.850000 NH1

ALY    HN 0.31 0.224500 H

ALY    CA 0.07 2.275000 CT1

ALY    HA 0.09 1.320000 HB 

ALY    CB -0.18 2.175000 CT2

ALY    HB1 0.09 1.320000 HA      

ALY    HB2 0.09 1.320000 HA

ALY    CG -0.18 2.175000 CT2 

ALY    HG1 0.09 1.320000 HA  

ALY    HG2 0.09 1.320000 HA 

ALY    CD -0.18 2.175000 CT2 

ALY    HD1 0.09 1.320000 HA 

ALY    HD2 0.09 1.320000 HA

ALY    CE 0.07 2.175000 CT2

ALY    HE1 0.09 1.320000 HA

ALY    HE2 0.09 1.320000 HA

ALY    NZ -0.47 1.850000 NH1

ALY    HZ 0.31 0.224500 H

ALY    C 0.51 2.000000 C

ALY    O -0.51 1.700000 O

ALY    CH3 -0.270 2.060000 CT3

ALY    HH31 0.090 1.320000 HA

ALY    HH32 0.090 1.320000 HA

ALY    HH33 0.090 1.320000 HA

ALY    CH 0.510 2.000000 C

ALY    OH -0.510 1.700000 O  

MN MN 2.00 1.710000 MN

SPO O1 -0.50 1.7000 O

SPO O2 -0.50 1.7000 O

I've changed the .pdb file for superoxide anion to something like this:

COMPND    SUPEROXIDE ANION

HETATM    1  O1   SPO     1      12.579  -7.067   0.000  1.00  0.00           O  

HETATM    2  O2   SPO     1      14.278  -7.067   0.000  1.00  0.00           O

CONECT    1    2                                                      

CONECT    2    1                                                      

MASTER        0    0    0    0    0    0    0    0    2    0    2    0

END

When I run pdb2pqr for the superoxide anion file, error occurred with the output:

Beginning PDB2PQR...

Parsed Amino Acid definition file.
Created protein object -
	Number of residues in protein: 1
	Number of atoms in protein   : 2
Setting the termini... 
Done.
Checking for missing heavy atoms... 
DEBUG INFO: PDBInputError src/routines.py: 621 
Error encountered: No heavy atoms found!

And when I run pdb2pqr for the protein file (with the acetylated lysine residue ALY) on my own computer, everything was alright until:

Checking if we must debump any residues...
Done.
Running propka and applying at pH 7.00... Traceback (most recent call last):
  File "<string>", line 62, in <module>
  File "C:\MinGW\msys\1.0\home\D3Y382\workspaces\github\apbs-pdb2pqr\pdb2pqr\bui
ld\pdb2pqr\out00-PYZ.pyz\main", line 668, in mainCommand
  File "C:\MinGW\msys\1.0\home\D3Y382\workspaces\github\apbs-pdb2pqr\pdb2pqr\bui
ld\pdb2pqr\out00-PYZ.pyz\main", line 326, in runPDB2PQR
  File "C:\MinGW\msys\1.0\home\D3Y382\workspaces\github\apbs-pdb2pqr\pdb2pqr\bui
ld\pdb2pqr\out00-PYZ.pyz\src.routines", line 1533, in runPROPKA
  File "C:\MinGW\msys\1.0\home\D3Y382\workspaces\github\apbs-pdb2pqr\pdb2pqr\bui
ld\pdb2pqr\out00-PYZ.pyz\propka30.Source.protein", line 325, in calculatePKA
  File "C:\MinGW\msys\1.0\home\D3Y382\workspaces\github\apbs-pdb2pqr\pdb2pqr\bui
ld\pdb2pqr\out00-PYZ.pyz\propka30.Source.protein", line 457, in calculateConfigu
rationPKA
  File "C:\MinGW\msys\1.0\home\D3Y382\workspaces\github\apbs-pdb2pqr\pdb2pqr\bui
ld\pdb2pqr\out00-PYZ.pyz\propka30.Source.determinants", line 253, in setBackBone
Determinants
  File "C:\MinGW\msys\1.0\home\D3Y382\workspaces\github\apbs-pdb2pqr\pdb2pqr\bui
ld\pdb2pqr\out00-PYZ.pyz\propka30.Source.determinants", line 266, in setBackBone
AcidDeterminants
KeyError: None

Could anybody kindly help me out of this two problems?

[Baker, Nathan]

Hi Kenneth --

I've asked Liz and Kyle to help you.

Thanks,

--
Nathan Baker
Laboratory Fellow and Technical Group Manager
Applied Statistics and Computational Modeling Group
Pacific Northwest National Laboratory
+1-509-375-3997
http://goo.gl/U9xu4t

------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=190641631&iu=/4140/ostg.clktrk
_______________________________________________
apbs-users mailing list
apbs-...@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/apbs-users

[Kenneth Cheng]

Dear Nathan,

Thank you very much for what you've done, although it seems that I've circumvented the problem. When I ran pdb2pqr on the web server for the protein with a ALY residue, the error simply disappeared (so there may be problem with my version of APBS installation on Windows); and I've manually written a pqr file and an input file for superoxide anion, with which I've successfully generated a dx file.

Thanks again!

--
Kenneth Cheng

在 2015年2月23日星期一 UTC+8下午12:04:20，Baker, Nathan写道：