AMBER Archive (2008)

Subject: RE: AMBER: protonated histidine ( charges in parm file versus all_a mino03.lib ). . .

From: Lwin, ThuZar (ThuZar.Lwin_at_stjude.org)
Date: Tue Mar 18 2008 - 11:45:49 CDT

Thank you Dr. Ross.
tz

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Ross Walker
Sent: Friday, March 14, 2008 11:30 AM
To: amber_at_scripps.edu
Subject: RE: AMBER: protonated histidine ( charges in parm file versus all_a mino03.lib ). . .

Hi Thu,

> I am wondering how the charges for protonated histidine (HIP)
> are generated with tleap.

tleap does not generate any charges - the charges are read from the lib
files. In the case of FF03 for regular residues this would be:

all_amino03.lib

for n terminal it would be

all_aminont94.lib

and for c terminal it would be

all_aminoct94.lib

> After all, I checked charges of
> HIP in all_amino03.lib with those generated in the parm
> file(considering the conversion factor of 18.2223) and I
> found out that the charges are not the same. Here is how I
> processed tleap.
>
> source leaprc.ff03
> w = loadPdb file.pdb
> saveAmberParm w file.parm file.rst
> quit
>
> In the end of the leaprc.ff03 file, I have edited
> #
> # assumed that most often proteins use HIE
> #
> HIS = HIP

This is a somewhat weird way to approach the problem. In general you should
edit your pdb file and change the residue names to the protonation state you
want them to be.

Here is a quick test that I tried:

$AMBERHOME/exe/tleap
source leaprc.ff03
mymol = copy HIP
saveamberparm mymol prmtop inpcrd

Using ambpdb to extract the charges from the prmtop

$AMBERHOME/exe/ambpdb -pqr -p prmtop < inpcrd

I get

REMARK HIP
ATOM 1 N HIP 1 3.326 1.548 0.000 -0.4250 1.550
ATOM 2 H HIP 1 3.909 0.724 0.000 0.2859 1.200
ATOM 3 CA HIP 1 3.970 2.846 0.000 0.3750 1.700
ATOM 4 HA HIP 1 3.672 3.400 -0.890 -0.0146 1.200
ATOM 5 CB HIP 1 3.577 3.654 1.232 -0.3321 1.700
ATOM 6 2HB HIP 1 2.497 3.801 1.241 0.1077 1.200
ATOM 7 3HB HIP 1 3.877 3.116 2.131 0.1077 1.200
ATOM 8 CG HIP 1 4.201 5.026 1.321 0.1824 1.700
ATOM 9 ND1 HIP 1 3.943 5.885 2.383 -0.0876 1.550
ATOM 10 HD1 HIP 1 3.340 5.692 3.170 0.3051 1.200
ATOM 11 CE1 HIP 1 4.624 6.998 2.183 -0.0131 1.700
ATOM 12 HE1 HIP 1 4.563 7.812 2.905 0.2306 1.200
ATOM 13 NE2 HIP 1 5.294 6.891 1.062 -0.1488 1.550
ATOM 14 HE2 HIP 1 5.896 7.605 0.677 0.3773 1.200
ATOM 15 CD2 HIP 1 5.059 5.679 0.492 -0.1921 1.700
ATOM 16 HD2 HIP 1 5.538 5.418 -0.451 0.2352 1.200
ATOM 17 C HIP 1 5.486 2.705 0.000 0.5666 1.700
ATOM 18 O HIP 1 6.009 1.593 0.000 -0.5604 1.500
TER
END

Column 9 is the charge - read from the prmtop file by ambpdb and divided by
18.2223.

Which, allowing for round off matches the definition of HIP in
all_amino03.lib

!entry.HIP.unit.atoms table str name str type int typex int resx int
flags
 int seq int elmnt dbl chg
 "N" "N" 0 1 131072 1 7 -0.424967
 "H" "H" 0 1 131072 2 1 0.285873
 "CA" "CT" 0 1 131072 3 6 0.375022
 "HA" "H1" 0 1 131072 4 1 -0.014621
 "CB" "CT" 0 1 131072 5 6 -0.332123
 "HB2" "HC" 0 1 131072 6 1 0.107725
 "HB3" "HC" 0 1 131072 7 1 0.107725
 "CG" "CC" 0 1 131072 8 6 0.182399
 "ND1" "NA" 0 1 131072 9 7 -0.087602
 "HD1" "H" 0 1 131072 10 1 0.305096
 "CE1" "CR" 0 1 131072 11 6 -0.013105
 "HE1" "H5" 0 1 131072 12 1 0.230635
 "NE2" "NA" 0 1 131072 13 7 -0.148766
 "HE2" "H" 0 1 131072 14 1 0.377295
 "CD2" "CW" 0 1 131072 15 6 -0.192052
 "HD2" "H4" 0 1 131072 16 1 0.235237
 "C" "C" 0 1 131072 17 6 0.566646
 "O" "O" 0 1 131072 18 8 -0.560417

So as far as I can tell this is working correctly. You should try taking a
clean amber tree (where leaprc files have not been modified etc) and then
edit your pdb to change the residue name from HIS to HIP and then repeat the
process and see what you get. I would also make sure you run the test cases
in $AMBERHOME/test to validate your compilation.

All the best
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu