Dear AMBER users,
I was trying to calculate the binding energy of my protein-ligand system
using binding_energy.mmpbsa.
The snapshots seem to be extracted correctly with appropriate box
information in the log file.
However while calculating the binding energy with the command below, it
shows the following message:
>$AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
/usr/apps/amber10//exe/sander -O -i sander_com.in -o sander_com.1.out -c
/data/MM-PBSA/EXTRACTS_CRD/snapshot_com.crd.1 -p
/data/MM-PBSA/gas_protein_lig.top not successful
In the meantime, I checked the sander_com.1.out file, where I came to know
about the information about the mismatch of NATOM.
FATAL: NATOM mismatch in coord and topology files.
I checked the total number of atoms for the solvated system, which is 35506
(including water, ions, ligand and protein) and for the gas phase system
(including ions, ligand and protein) is 3223. I used the NTOTAL as 35506.
But I dont understand why sander complaints about the mismatch of NATOM.
Any suggestions on this regard is highly appreciated.
FYI, I have copied the contents of log file in this text. please check it
below.
=>> Init data
Presuming executables of amber suite to be in /usr/apps/amber10//exe
=>> Reading input parameters
Found PREFIX => snapshot
Found PATH => /data/meher/MM-PBSA-HIV/3EM6-DAR/EXTRACTS_CRD
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => /data/MM-PBSA/gas_protein_lig.top
Found RECPT => /data/MM-PBSA/gas_protein.top
Found LIGPT => /data/MM-PBSA/gas_lig.top
Found GC => 1
Found AS => 0
Found DC => 0
Found MM => 0
Found GB => 0
Found PB => 0
Found MS => 0
Found NM => 0
Found BOX => YES
Found NTOTAL => 35506
Found NSTART => 1
Found NSTOP => 1000
Found NFREQ => 20
Found NUMBER_LIG_GROUPS => 1
Found LSTART => 3142
Found LSTOP => 3216
Found NUMBER_REC_GROUPS => 1
Found RSTART => 1
Found RSTOP => 3141
Found TRAJECTORY => /data/MM-PBSA/prod_12ns.mdcrd
=>> Checking sanity
Checking GENERAL
Setting START to default 1
Setting STOP to default 10e10
Setting OFFSET to default 1
Setting VERBOSE to default 0
Checking GC
Checking TRAJ
=>> Creating input
make_crd input
=>> Creating coordinates
Executing makecrd
Amber8 Module: make_crg_hg
usage: make_crd_hg < trajectory_file
Box info found: 77.2540000000000 77.2540000000000
77.2540000000000
Box info found: 77.2910000000000 77.2910000000000
77.2910000000000
Box info found: 77.2880000000000 77.2880000000000
77.2880000000000
Box info found: 77.2910000000000 77.2910000000000
77.2910000000000
Box info found: 77.2880000000000 77.2880000000000
77.2880000000000
Box info found: 77.2680000000000 77.2680000000000
77.2680000000000
Box info found: 77.2780000000000 77.2780000000000
77.2780000000000
Box info found: 77.2670000000000 77.2670000000000
77.2670000000000
Box info found: 77.3040000000000 77.3040000000000
77.3040000000000
Box info found: 77.3030000000000 77.3030000000000
77.3030000000000
Box info found: 77.2960000000000 77.2960000000000
77.2960000000000
Thanks
Siddharth
On Thu, Sep 2, 2010 at 2:48 PM, Siddharth Rastogi <
siddharthrastogi08.gmail.com> wrote:
> Thanks Jason.
> I tried with the commands you suggested and it is working now.
>
> Thank you once again.
>
> Siddharth
>
>
>
>
>
> On Wed, Sep 1, 2010 at 9:30 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> Hello,
>>
>> On Wed, Sep 1, 2010 at 8:18 PM, Siddharth Rastogi <
>> siddharthrastogi08.gmail.com> wrote:
>>
>> > Hello Dwight & Jason,
>> >
>> > Thank you for your valuable suggestions.
>> > Yeah, I have applied all the bug fixes for AMBER 10 version.
>> >
>> > Also I set the AMBERHOME in addition to the bug fixes, but the same
>> problem
>> > persists.
>> >
>> > The command I followed are as follows:
>> >
>> > $ set AMBERHOME=/usr/apps/amber10/
>> > $ export AMBERHOME
>> > $ $AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log
>> > -bash: /exe/mm_pbsa.pl: No such file or directory
>> >
>>
>> This right here tells you that $AMBERHOME returns nothing, since it's
>> complaining that "/exe/mm_pbsa.pl" can't be found. Do not use the "set"
>> statement above. Try the following:
>>
>> export AMBERHOME=/usr/apps/amber10
>> $AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log
>>
>> If you want to check that AMBERHOME has actually been set, use the
>> following
>> command:
>>
>> /usr/bin/env | grep AMBERHOME
>>
>> Good luck!
>> Jason
>>
>> >
>> > Again I did like as before, but the same. I couldn't go elsewhere.
>> >
>> > $ /usr/apps/amber10/exe/mm_pbsa.pl extract_coords.mmpbsa >
>> > extract_coords.log
>> >
>> > Use of uninitialized value in concatenation (.) or string at
>> > /usr/apps/amber10/exe/mm_pbsa.pl line 22.
>> > Can't locate mm_pbsa_global.pm in .INC (.INC contains: /src/mm_pbsa
>> > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
>> > /usr/lib64/perl5/site_perl/5.8.7/x86_64-linux-thread-multi
>> > /usr/lib64/perl5/site_perl/5.8.6/x86_64-linux-thread-multi
>> > /usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi
>> > /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl/5.8.7
>> > /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5
>> > /usr/lib/perl5/site_perl
>> > /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
>> > /usr/lib64/perl5/vendor_perl/5.8.7/x86_64-linux-thread-multi
>> > /usr/lib64/perl5/vendor_perl/5.8.6/x86_64-linux-thread-multi
>> > /usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi
>> > /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl/5.8.7
>> > /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5
>> > /usr/lib/perl5/vendor_perl
>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
>> > /usr/lib/perl5/5.8.8 .) at /usr/apps/amber10/exe/mm_pbsa.pl line 23.
>> > BEGIN failed--compilation aborted at /usr/apps/amber10/exe/mm_pbsa.plline
>> > 23.
>> >
>> > Any more suggestions is always appreciated.
>> >
>> > Thanks
>> > Siddharth
>> >
>> >
>> > On Wed, Sep 1, 2010 at 9:31 AM, Dwight McGee <dwight.mcgee.gmail.com>
>> > wrote:
>> >
>> > > Hi,
>> > >
>> > > Have you applied all the bug fixes?
>> > >
>> > > On Wed, Sep 1, 2010 at 11:10 AM, Siddharth Rastogi <
>> > > siddharthrastogi08.gmail.com> wrote:
>> > >
>> > > > Dear AMBER users,
>> > > >
>> > > > I am doing some MM-PBSA Calculation for my protein-ligand complex.
>> > > > However, I was just following the tutorial in the AMBER web page by
>> > Ross
>> > > > Walker.
>> > > > In the mean time I got the error as follows:
>> > > >
>> > > > Use of uninitialized value in concatenation (.) or string at
>> > > > /usr/apps/amber10/exe/mm_pbsa.pl line 22.
>> > > > Can't locate mm_pbsa_global.pm in .INC (.INC contains: /src/mm_pbsa
>> > > > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
>> > > > /usr/lib64/perl5/site_perl/5.8.7/x86_64-linux-thread-multi
>> > > > /usr/lib64/perl5/site_perl/5.8.6/x86_64-linux-thread-multi
>> > > > /usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi
>> > > > /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl/5.8.7
>> > > > /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5
>> > > > /usr/lib/perl5/site_perl
>> > > > /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
>> > > > /usr/lib64/perl5/vendor_perl/5.8.7/x86_64-linux-thread-multi
>> > > > /usr/lib64/perl5/vendor_perl/5.8.6/x86_64-linux-thread-multi
>> > > > /usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi
>> > > > /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl/5.8.7
>> > > > /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5
>> > > > /usr/lib/perl5/vendor_perl
>> > > /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
>> > > > /usr/lib/perl5/5.8.8 .) at /usr/apps/amber10/exe/mm_pbsa.pl line
>> 23.
>> > > > BEGIN failed--compilation aborted at
>> > /usr/apps/amber10/exe/mm_pbsa.plline
>> > > > 23.
>> > > >
>> > > >
>> > > >
>> > > > I didn't understand the full error message.
>> > > > So I tried to find it out from the AMBER mailing list.
>> > > > I got one same type of posting (
>> > > > http://archive.ambermd.org/200809/0335.html),
>> > > > but unfortunately no reply to this question.
>> > > >
>> > > > I have also this problem with both amber 9 and 10.
>> > > > Is it a problem with the installation ?
>> > > > So can any one suggest, what is going on here.
>> > > > Thank you for your suggestions.
>> > > >
>> > > >
>> > > > Thanks
>> > > >
>> > > > --
>> > > > Siddharth Rastogi
>> > > > _______________________________________________
>> > > > AMBER mailing list
>> > > > AMBER.ambermd.org
>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > T. Dwight McGee Jr.
>> > > Quantum Theory Project
>> > > University of Florida
>> > > Graduate Student
>> > > dwight.mcgee.gmail.com
>> > >
>> > > "Problems cannot be solved at the same level of awareness that created
>> > > them."
>> > > Albert Einstein
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> >
>> >
>> >
>> > --
>> > Siddharth Rastogi
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Siddharth Rastogi
>
--
Siddharth Rastogi
_______________________________________________
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Received on Fri Sep 03 2010 - 17:30:03 PDT
