AMBER Archive (2009)

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

From: Hannes Kopitz (Hannes.Kopitz_at_gmx.de)
Date: Fri Dec 04 2009 - 04:45:10 CST

Dear Antonija,

Try the following:
Go to your $AMBERHOME/src/sander directory and open the file mdread.f
Search the section in the code containing the following lines (about line 1565):

               x(L165-1+i) = 1.18d0 + 1.4d0
            else
               write( 0,* ) 'bad atom type: ',atype

Change it to:

               x(L165-1+i) = 1.18d0 + 1.4d0
            else if (atype == 'Zn') then
               x(L165-1+i) = 1.22d0 + 1.4d0
            else
               write( 0,* ) 'bad atom type: ',atype

Then recompile sander and try again.

Good luck!
Hannes

-------- Original-Nachricht --------
> Datum: Fri, 04 Dec 2009 10:27:31 +0100
> Von: "Antonija Tomić" <Antonija.Tomic_at_irb.hr>
> An: AMBER List <amber_at_ambermd.org>
> Betreff: [AMBER] mm_pbsa- Decomposition: bad atom type

> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber 

-- 
GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT!
Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber