AMBER Archive (2009)

Subject: [AMBER] mm_pbsa- Decomposition: bad atom type

From: Antonija Tomić (Antonija.Tomic_at_irb.hr)
Date: Fri Dec 04 2009 - 03:27:31 CST

Dear Amber Users,

in October I tried to ask you question regarding MM/GBSA-PBSA in
amber10. I have problems with running energy decomposition.
No one answered to my question in October so I will try to make the
same question again (I copy-paste the letter from October).
I will appreciate any help.

Thanks in advance.

Antonija

Letter from October:

Dear Amber Users,

I am using MM/GBSA of amber10 to calcluate binding energy of
protein/ligand system. There is one Zn atom in the protein.
Binding calculation is working fine. But I got "bad atom type:
Zn" when I run energy decomposition. And I have already add "ZN" =>
1.22 + 1.400,"
to the script of mm_pbsa_calceneent.pm according to the mail list.

I have also tried to set MS to a non-zero value in my mm_pbsa input
but then I get error massage:

Died at /usr/local/amber10/src/mm_pbsa/mm_pbsa_readinput.pm line 354.

And the line 354 says:

  if($r_gen->{"DC"} > 0 && ($r_gen->{"GC"} > 0 ||
                             $r_gen->{"AS"} > 0 ||
                             $r_gen->{"NM"} > 0 ||
                             $r_gen->{"MS"} > 0)){
     print " Energy decomp is not (yet) possible with GC, AS, NM, MS\n";
     die();

Here is the input file:

#
# Input parameters for mm_pbsa.pl
# This example does decomposition by pairwise residues
#
# Holger Gohlke
# 08.01.2002
#
################################################################################
@GENERAL
#
# General parameters
# 0: means NO; >0: means YES
#
PREFIX snapshot_RRNA
PATH ../extract_coords/
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../RRNAmd2min.top
RECPT ../ENZmd2min.top
LIGPT ../LIGmd2min.top
#
GC 0
AS 0
DC 1
#
MM 1
GB 1
PB 0
MS 0
#
NM 0
#
################################################################################
@DECOMP
#
DCTYPE 4
#
COMREC 297-297 369-369 402-405 447-447 448-448 452-452
505-505 563-563 565-565
COMLIG 725-725
COMPRI 297-297 369-369 402-405 447-447 448-448 452-452
505-505 563-563 565-565 725-725
RECRES 297-297 369-369 402-405 447-447 448-448 452-452
505-505 563-563 565-565
RECPRI 297-297 369-369 402-405 447-447 448-448 452-452
505-505 563-563 565-565
RECMAP 297-297 369-369 402-405 447-447 448-448 452-452
505-505 563-563 565-565
LIGRES 1-1
LIGPRI 1-1
LIGMAP 725-725
#
################################################################################
@MM
#
IGB 2
GBSA 2
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################

I would be very grateful for any advice.
Thanks in advance.

Antonija

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