AMBER Archive (2009)

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

From: Antonija Tomić (Antonija.Tomic_at_irb.hr)
Date: Fri Dec 04 2009 - 04:57:59 CST

Dear Hannes,

thank you for your quick answer. I will try that.

Antonija

Citiram Hannes Kopitz <Hannes.Kopitz_at_gmx.de>:

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