AMBER Archive (2006)

Subject: Re: AMBER: mm_pbsa: binding energy calculation

From: Angelo (angelo_at_holmes.cancres.nottingham.ac.uk)
Date: Mon Oct 30 2006 - 03:36:25 CST

Hi,

You are wellcome. Be sure that you create the right topology file for
your ligand ( if you checked it with VMD should be OK) and that you
specify the right path for your topology file and coordinate files.

Angelo

Varsha Goyal wrote:

>Thanks Angelo,
>It solved my problem but now when I am running
>binding_energy.mmpbsa evertime it causes some problem
>with my ligand file.
>Error looks like this:
>
>/usr/local/amber8/exe/pbsa -O -i pbsa.in -o
>pbsa_lig.1.out -c ./extract_coord/snapshot_lig.crd.1
>-p ./prmtop.ets not successful
>
>I am not sure where should I look because when I look
>at the structure for this trajectory in VMd it looks
>fine to me.
>Can you or someone else please suggest solution to
>this problem?
>
>Thanks in advance,
>Varsha
>
>
>--- Angelo <angelo_at_holmes.cancres.nottingham.ac.uk>
>wrote:
>
>
>
>>Hi,
>>
>>If you are using Molsurf (from your script it seems
>>so) to calculate the
>>non polar solavtion free energy you should go to
>>the
>>"mm_pbsa_calceneent.pm" Perl Module in your mm_pbsa
>>directory ( mine is:
>>"/usr/local/amber9-x86_64/src/mm_pbsa") and add the
>>Zn Bondi radius here:
>>
>># Bondi radii + 1.4A and probe radius of 0.0A yields
>>SAS
>> # Bondi radii + 0.0A and probe radius of 1.4A
>>yields molecular surface
>> # Bondi radii + 0.0A and probe radius of 0.0A
>>yields vdW surface
>> 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,
>> "FE" => 1.300 + 1.400,
>> "Zn" => you know it + 1.400
>> "Na+" => 1.200 + 1.400,
>> "Cl-" => 1.700 + 1.400,
>> "MG" => 1.180 + 1.400,
>> );
>>Hope it helps
>>
>>Angelo fro Nottingham
>>
>>
>>Varsha Goyal wrote:
>>
>>
>>
>>>Dear Amber Developers and Users,
>>>
>>>I am trying to calculate Binding energy of protein
>>>
>>>
>>and
>>
>>
>>>Ligand. I was following the tutorial writeen by Dr.
>>>Holger Gohlke. In my case I have a "ZN" ion in the
>>>active site. When I prepared my topology files for
>>>protein and complex I loaded parameters for Zn and
>>>also lib file for Zn. During simulations it never
>>>raised any error, but now when I am trying to
>>>
>>>
>>estimate
>>
>>
>>>binding energy it is giving me following error:
>>>
>>>" No radius found for Zn 4042 in residue ZNC
>>>
>>>
>>259"
>>
>>
>>>where ZNC is name of residue for Zn ion.
>>>
>>>Here is my binding_energy.log file
>>>
>>>=>> Init data
>>> Presuming executables of amber suite to be in
>>>/usr/local/amber8/exe
>>>
>>>=>> Reading input parameters
>>> Found PREFIX => snapshot
>>> Found PATH => ./extract_coord
>>> Found COMPLEX => 1
>>> Found RECEPTOR => 1
>>> Found LIGAND => 1
>>> Found COMPT => ./prmtop.com
>>> Found RECPT => ./prmtop.prot
>>> Found LIGPT => ./prmtop.ets
>>> Found GC => 0
>>> Found AS => 0
>>> Found DC => 0
>>> Found MM => 1
>>> Found GB => 1
>>> Found PB => 1
>>> Found MS => 1
>>> Found NM => 0
>>> Found PROC => 2
>>> Found REFE => 0
>>> Found INDI => 1.0
>>> Found EXDI => 80.0
>>> Found SCALE => 2
>>> Found LINIT => 1000
>>> Found PRBRAD => 1.4
>>> Found ISTRNG => 0.0
>>> Found RADIOPT => 0
>>> Found NPOPT => 1
>>> Found CAVITY_SURFTEN => 0.0072
>>> Found CAVITY_OFFSET => 0.00
>>> Found SURFTEN => 0.0072
>>> Found SURFOFF => 0.00
>>> Found DIELC => 1.0
>>> Found IGB => 2
>>> Found GBSA => 1
>>> Found SALTCON => 0.00
>>> Found EXTDIEL => 80.0
>>> Found INTDIEL => 1.0
>>> Found SURFTEN => 0.0072
>>> Found SURFOFF => 0.00
>>> Found PROBE => 0.0
>>> Found SANDER =>
>>>/usr/local/amber8/exe-serial/sander
>>>
>>>=>> Checking sanity
>>> Checking GENERAL
>>> Checking MM
>>> Checking PB
>>> Checking GB
>>> Checking MS
>>>
>>>=>> Creating input
>>> Sander input
>>> PBSA input
>>>
>>>=>> Calculating energy / entropy contributions
>>> Calc contrib for
>>>./extract_coord/snapshot_com.crd.1
>>> Calc MM/GB/SAS
>>> Generate PDB
>>> Center PDB
>>> Calc PBSA
>>> Generate PQR
>>> No radius found for Zn 4042 in residue
>>>
>>>
>>ZNC
>>
>>
>>>259
>>>
>>>Can someone please help me out in thir problem
>>>
>>>
>>because
>>
>>
>>>I am not sure where can i define radius of Zn now.
>>>
>>>Here is files related to Zn, which i used while
>>>creating topology files and coordinate files.
>>>
>>>
>>>
>>##############ZNC.lib###############################
>>
>>
>>>!!index array str
>>>"ZNC"
>>>!entry.ZNC.unit.atoms table str name str type
>>>
>>>
>>int
>>
>>
>>>typex int resx int flags int seq int elmnt dbl
>>>chg
>>>"Zn" "Zn" 0 1 131075 1 30 0.866000
>>>!entry.ZNC.unit.atomspertinfo table str pname str
>>>ptype int ptypex int pelmnt dbl pchg
>>>"Zn" "Zn" 0 -1 0.0
>>>!entry.ZNC.unit.boundbox array dbl
>>>-1.000000
>>>0.0
>>>0.0
>>>0.0
>>>0.0
>>>!entry.ZNC.unit.childsequence single int
>>>263
>>>!entry.ZNC.unit.connect array int
>>>0
>>>0
>>>!entry.ZNC.unit.hierarchy table str abovetype int
>>>abovex str belowtype int belowx
>>>"U" 0 "R" 1
>>>"R" 1 "A" 1
>>>!entry.ZNC.unit.name single str
>>>""
>>>!entry.ZNC.unit.positions table dbl x dbl y dbl
>>>
>>>
>>z
>>
>>
>>>-6.788000 -1.621000 15.381000
>>>!entry.ZNC.unit.residueconnect table int c1x int
>>>
>>>
>>c2x
>>
>>
>>>int c3x int c4x int c5x int c6x
>>>0 0 0 0 0 0
>>>!entry.ZNC.unit.residues table str name int seq
>>>
>>>
>>int
>>
>>
>>>childseq int startatomx str restype int imagingx
>>>"ZNC" 262 2 1 "?" 0
>>>!entry.ZNC.unit.residuesPdbSequenceNumber array int
>>>1
>>>!entry.ZNC.unit.solventcap array dbl
>>>-1.000000
>>>0.0
>>>0.0
>>>0.0
>>>0.0
>>>!entry.ZNC.unit.velocities table dbl x dbl y dbl
>>>
>>>
>>z
>>
>>
>>>0.0 0.0 0.0
>>>#################################################
>>>
>>>
>>------------------------------------------------------
>>
>>
>>>##############frcmod.znc###########################
>>>This frcmod file is for ZNC (zinc 2+ ion).
>>>MASS
>>>ZNC 65.4
>>>
>>>NONB
>>>ZNC 1.10 0.0125
>>>
>>>Thanks in advance,
>>>Varsha Gupta
>>>
>>>__________________________________________________
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>>>
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>>
>>
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>>>
>>>
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>
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