Dear AMBER users
1)Successful in running the AMBER tutorials recommended for calculating binding free energy for Estrogen -Raloxifene
2) Extending the same concept of calculating the binding free for my ligand (geldanamycin) and protein (1A4H) complex
3) Though the ligand (coordinates separated out from the pdb file), initially failed in generating the parameter files (prmtop and inpcrd files), after optimizing it through GAUSSIAN, successful in generating these files
4)NOT ABLE to generate the parameter files (prmtop and inpcrd) for the protein ligand complex, even after loading the lib file of geldanamycin
5) Showing error while generating the prmtop and inpcrd files for the protein-ligand complex
6) Attaching the following files which I have used
(i) 1A4H_gelda.pdb
(ii) gelda_opt.pdb
(iii) error_1.txt (while executing: complex = loadpdb 1A4H_gelda.pdb)
(iv) error_2.txt (while executing: saveamberparm complex 1A4H_gelda.prmtop 1A4H_gelda.inpcrd)
Request you to advice me where I am going wrong
With best of regards
Ramesh K V
________________________________
From: kureeckal ramesh <kureeckalramesh.yahoo.co.in>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Thursday, 1 March 2012 4:00 PM
Subject: error in sander_com.1.out
Dear Nadine
Thank you for the reply. I saw the sander_com.1.out file and the error message is as follows
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
FATAL: NATOM mismatch in coord and topology files
-------------------------------------------------------------------------------------------------------------
Please suggest some solution
Regards
Ramesh K V
________________________________
From: "Nadine.Homeyer.uni-duesseldorf.de" <Nadine.Homeyer.uni-duesseldorf.de>
To: kureeckal ramesh <kureeckalramesh.yahoo.co.in>; AMBER Mailing List <amber.ambermd.org>
Sent: Thursday, 1 March 2012 3:21 PM
Subject: Re: [AMBER] problem with MMPBSA script
The execution of Sander for the calculation of MM, GB, or SAS was not
sucessful.
Set VERBOSE to 1 in the MM-PBSA input file and re-run the energy calculation.
Then have a look into the sander_com.1.out file for the error messages created
by Sander.
A
description of this and other error messages can be found at
http://ambermd.org/Questions/mm_pbsa.html
Best regards,
Nadine
Zitat von kureeckal ramesh <kureeckalramesh.yahoo.co.in>:
>
>
> Dear AMBER users
>
> 1) I have completed 10ns os MD simulation for one of my protein
> solvated with water (no drug interaction).
>
> 2) Now I am interested in free energy calculation for which which I
> followed the extracts_coords.mmpbsa and binding_energy.mmpbsa as
> recommeded in the tuotrial for amber
> (http://ambermd.org/tutorials/advanced/tutorial3/section3.htm)
> 3) Since I am working
with only protein solvated with water, the
> above 2 scripts were changed accordingly and is shown below.
>
> 4) Though extracts_coords.mmpbsa was generate the several snapshot
> files, I was not able to succedd with bindign_energy calcaulation
> using binding_energy.mmpbsa script AS THE OUTPUT showed error
>
>
> SCRIPT DETAILS
>
> I . extracts_coords.mmpbsa
> --------------------------------------------------------------------------------------------------------------------
> -------------------------------------------------------------------------------------------------------------------
> PREFIX snapshot
> PATH ./
> #
>
COMPLEX 1
> RECEPTOR 0
> LIGAND 0
>
> COMPT ./2NPD_solvated.prmtop
> #RECPT ./2NPD.prmtop
>
> #
> GC 1
> AS 0
> DC
0
> #
> MM 0
> GB 0
> PB 0
> MS 0
> #
> NM 0
> #
> ################################################################################
> .MAKECRD
> #
> BOX YES
>
NTOTAL 42193
> NSTART 1
> NSTOP 200
> NFREQ 1
> #
> NUMBER_LIG_GROUPS 0
> #LSTART 2622
> #LSTOP 3862
> NUMBER_REC_GROUPS 1
> RSTART 1
>
RSTOP 2621
> #
> #################################################################################
> .TRAJECTORY
> #
> TRAJECTORY ./prod1.mdcrd
> TRAJECTORY ./prod2.mdcrd
> TRAJECTORY ./prod3.mdcrd
> TRAJECTORY ./prod4.mdcrd
> TRAJECTORY ./prod5.mdcrd
> TRAJECTORY ./prod6.mdcrd
> TRAJECTORY ./prod7.mdcrd
>
TRAJECTORY ./prod8.mdcrd
> TRAJECTORY ./prod9.mdcrd
> TRAJECTORY ./prod10.mdcrd
> TRAJECTORY ./prod11.mdcrd
> TRAJECTORY ./prod12.mdcrd
> TRAJECTORY ./prod13.mdcrd
> TRAJECTORY ./prod14.mdcrd
> TRAJECTORY ./prod15.mdcrd
> TRAJECTORY ./prod16.mdcrd
>
TRAJECTORY ./prod17.mdcrd
> TRAJECTORY ./prod18.mdcrd
> TRAJECTORY ./prod19.mdcrd
> TRAJECTORY ./prod20.mdcrd
> -----------------------------------------------------------------------------------------------------------
> ----------------------------------------------------------------------------------------------------------
>
>
> II. binding_energy.mmpbsa
> ----------------------------------------------------------------------------------------------------------
> ---------------------------------------------------------------------------------------------------------#
>
PREFIX snapshot
> PATH ./
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 0
> #
> COMPT ./2NPD_solvated.prmtop
> RECPT ./2NPD.prmtop
>
> #
> GC 0
>
AS 0
> DC 0
> #
> MM 1
> GB 1
> PB 1
> MS 1
> #
> NM 0
> #
>
################################################################################
> .PB
> #
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 2
> LINIT 1000
> PRBRAD 1.4
>
ISTRNG 0.0
> RADIOPT 0
> NPOPT 1
> CAVITY_SURFTEN 0.0072
> CAVITY_OFFSET 0.00
> #
> SURFTEN 0.0072
> SURFOFF 0.00
> #
> ################################################################################
> .MM
> #
> DIELC 1.0
> #
>
################################################################################
> .GB
> #
> IGB 2
> GBSA 1
> SALTCON 0.00
> EXTDIEL 80.0
> INTDIEL 1.0
> #
> SURFTEN 0.0072
> SURFOFF 0.00
> #
>
################################################################################
> .MS
> #
> PROBE 0.0
> #
> ----------------------------------------------------------------------------------------------------------------------
> ----------------------------------------------------------------------------------------------------------------------
> error after running binding energycommand
> ramesh.sgiUV:~> mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
> /data1/apps/amber/10/intel-mkl-openmpi/exe/sander -O -i
> sander_com.in -o sander_com.1.out -c ./snapshot_com.crd.1 -p
> ./2NPD_solvated.prmtop not successful
>
>
> details of the binding_energy.log file
>
--------------------------------------------------
>
> =>> Init data
> Presuming executables of amber suite to be in
> /data1/apps/amber/10/intel-mkl-openmpi/exe
>
> =>> Reading input parameters
> Found PREFIX => snapshot
> Found PATH => ./
> Found COMPLEX => 1
> Found RECEPTOR => 0
> Found LIGAND => 0
> Found COMPT => ./2NPD_solvated.prmtop
> Found RECPT => ./2NPD.prmtop
> 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
>
> =>> 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 MM
> Checking PB
> Checking GB
> Checking MS
>
> =>> Creating input
> Sander input
> PBSA input
>
> =>> Calculating energy / entropy contributions
> Calc contrib for ./snapshot_com.crd.1
>
Calc MM/GB/SAS
> ----------------------------------------------------------------------
>
>
> Resquest you to kindly suggest where I should make corrections in the
> script to calculate the binding free energy between the protein and
> the water ONLY
>
>
> Thanking you
> Ramesh K V
> Dept of Biotech
> Jain University Bangalore
>
>
>
>
>
>
>
> ________________________________
> From: kureeckal ramesh <kureeckalramesh.yahoo.co.in>
> To: "amber.ambermd.org" <amber.ambermd.org>
> Cc: "sudhadeshmukh.yahoo.com" <sudhadeshmukh.yahoo.com>
> Sent: Thursday, 1 December 2011 10:44 AM
> Subject:
>
>
> Dear amber user
>
> As a part of sustival tutorial (MD simulation of protein-drug
> interaction), I was able to generate sustiva.mol2 file.
> Got an error while proceeding further (i. e, after executing tleap
> command) which is as follows
>
> ---------------------------------------------------------------------
>> SUS = loadmol2 sustiva.mol2
> Loading Mol2 file: ./sustiva.mol2
> Reading MOLECULE named SUS
> /data1/apps/amber/10/intel-mkl-openmpi/exe/tleap: line 8: 25824
> Segmentation fault
> /data1/apps/amber/10/intel-mkl-openmpi/bin/teLeap
>
-I/data1/apps/amber/10/intel-mkl-openmpi/dat/leap/prep
> -I/data1/apps/amber/10/intel-mkl-openmpi/dat/leap/lib
> -I/data1/apps/amber/10/intel-mkl-openmpi/dat/leap/parm
> -I/data1/apps/amber/10/intel-mkl-openmpi/dat/leap/cmd
> $*
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> looking forward for your help
>
> With regards
> Ramesh K V
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Apr 23 2012 - 02:30:03 PDT
