AMBER Archive (2008)

Subject: AMBER: MM-PBSA : bad atom type: ZN

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Mon Dec 08 2008 - 10:51:12 CST

Dear any amber users,

I have a problem, as shown below in MM-PB(GB)SA, on decompose energy of a
metalloprotein system that contains protein (resi 1- 317), substrate ligand
(resid 318-322) and one ZN atom (resid 323). It warns about "bad atom type:
ZN". I also try to fix by adding a parameter line for ZN in
mm_pbsa_calceneent.pm (see below) but it doesn't help. Anyway, I am not sure
that I set the input file when generate crd file correctly because my
substrate ligand is located between protein and ZN which is different from
other previous tutorial. This is my mistake on setting up in MD
simulation. As long I search for this problem on google, I found ths similar
problem but I don't know the parameter (bondi radius) for ZN to put
in Amber9/src/sander/mdread.f. This problem might easily from you.

So I also attached all necessary files for this calculation, please see
below.

If anyone can figure out or give me a good suggestion on the source this
problem, I would be appreciated on any help.

Thanks in advance.

Jitrayut Jitonnom

Here is my error in decompose energy, (generate crd look fine !!! 40
snapshots)

 =>> Creating input
    Sander input
=>> Calculating energy / entropy contributions
    Calc contrib for ../01_generate_snapshot/snapshot_com.crd.1
        Calc MM/GB/SAS
 bad atom type: ZN
        /home/program/amber9/exe/sander -O -i sander_com.in -o
sander_com.1.out -c ../01_generate_snapshot/snapshot_com.crd.1 -p
../enz-lig.top not successful

  Thisi is mm_pbsa_calceneent.pm

sub generate_pqr(){
###################
  my %exp_rad = (
                 "N" => 1.550 + 1.400,
                 "H" => 1.200 + 1.400,
                 "C" => 1.700 + 1.400,
                 "O" => 1.500 + 1.400,
                 "P" => 1.800 + 1.400,
                 "S" => 1.800 + 1.400,
                 "*ZN" => 1.100 + 1.400*, ! Am I correct
for this Zn value ?
                 "FE" => 1.300 + 1.400,
                 "Na+" => 1.200 + 1.400,
                 "Cl-" => 1.700 + 1.400,
                 "MG" => 1.180 + 1.400,

This is extract_coords.mmpbsa
.
.
@MAKECRD
BOX YES
NTOTAL 60482
NSTART 3001
NSTOP 5000
NFREQ 50
#
NUMBER_LIG_GROUPS 1
LSTART 4894
LSTOP 4981
NUMBER_REC_GROUPS 2
RSTART 1
RSTOP 4893
RSTART 4982
RSTOP 4982
.
.

This is decompose_energy.mmpbsa
.
.
@DECOMP
DCTYPE 2
#
COMREC 1-317 323-323
COMLIG 318-322
COMPRI 1-323
RECRES 1-317 323-323
RECPRI 1-317 323-323
RECMAP 1-317 323-323
LIGRES 1-5
LIGPRI 1-5
LIGMAP 318-322
.
.

This is the pdb file.

ATOM 1 N ASN 1 -15.699 -22.907 6.655 1.00 0.00
! ......... enzyme
ATOM 2 H1 ASN 1 -15.047 -22.298 6.182 1.00 0.00
! ......... enzyme
ATOM 3 H2 ASN 1 -15.297 -23.191 7.537 1.00 0.00
! ......... enzyme
ATOM 4 H3 ASN 1 -16.616 -22.483 6.630 1.00 0.00
! ......... enzyme
.
.
ATOM 4891 C GLU 317 -4.911 2.950 -30.982 1.00 0.00
! ......... enzyme
ATOM 4893 OXT GLU 317 -3.867 3.464 -31.379 1.00 0.00
! ......... enzyme
TER
ATOM 4894 N ILE 318 0.791 9.719 8.333 1.00 0.00
! ......... ligand
.
.
ATOM 4915 N PRO 319 1.212 6.074 7.980 1.00 0.00
! ......... ligand
.
.
ATOM 4929 N TYR 320 3.634 4.479 5.717 1.00 0.00
! ......... ligand
.
.
ATOM 4950 N VAL 321 1.871 3.870 2.880 1.00 0.00
!! ......... ligand
.
.
ATOM 4979 C GLU 322 3.697 2.651 -1.296 1.00 0.00
! ......... ligand
ATOM 4980 O GLU 322 4.153 3.361 -0.381 1.00 0.00
! ......... ligand
ATOM 4981 OXT GLU 322 4.414 2.172 -2.196 1.00
0.00! ......... ligand
TER
ATOM 4982 ZN ZNA 323 1.314 -0.290 -0.077 1.00 0.00
! ......... enzyme
TER

c --- construct parameters for SA calculation; note that the
c radii stored in L165 are augmented by 1.4 Ang.

I added the following code in Amber9/src/sander/mdread.f (cl actually not
needed, but it is treated as carbon otherwise):
! Cl added by UR 5/11-08: radius = 1.8, parameters from S
            else if (atype == 'Cl' .or. atype(1:1) == 'cl') then
               x(l165-1+i) = 1.80d0 + 1.4d0
               x(l170-1+i) = 0.54581d0
               x(l175-1+i) = -0.19477d0
               x(l180-1+i) = -0.0012873d0
               x(l185-1+i) = 0.00029247d0
! F added by UR 5/11-08: Bondi radius and parameters from O nbond=1
            else if (atype(1:1) == 'F' .or. atype(1:1) == 'f') then
                  x(l165-1+i) = 1.47d0 + 1.4d0
                  x(l170-1+i) = 0.77914d0
                  x(l175-1+i) = -0.25262d0
                  x(l180-1+i) = -0.0016056d0
                  x(l185-1+i) = 0.00035071d0

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