Dear Jason,
In two out of three times I got the following error
FATAL: NATOM mismatch in coord and topology files
while for third case there is no specific error mentioned but it sopped after the following lines
Processing frame 1
iter Total bad vdW elect nonpolar genBorn frms
eff.c(2713) enb14 --> nan
eff.c(2714) eel14 --> nan
eff.c(2772) enb --> nan
eff.c(2773) eel --> nan
eff.c(2774) e_gb --> nan
eff.c(2775) esurf --> 54.851
eff.c(2776) evdwnp --> 0.000
ff: 0 nan nan nan nan 54.85 nan nan
regards,
Nitin Sharma
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Thursday, April 24, 2014 10:31 PM
To: amber.ambermd.org
Subject: Re: [AMBER] MMPBSA error
On Thu, 2014-04-24 at 22:05 +0800, Nitin Sharma wrote:
> Dear amber users,
>
> I have been preparing files for MD with following protocol and then
> later calculating MM/GBSA. I have been doing that with lot of files
> BUT recently I encountered error in two files while calculating
> binding free energy. Can you tell me what is wrong
>
> # Ligand preparation using antechamber antechamber -i ligand.pdb -fi
> pdb -o ligand.mol2 -fo mol2 -c bcc -s 2 -nc {charge of the ligand}
> parmchk -i ligand.mol2 -f mol2 -o ligand.frcmod
>
> #leaprc
> source leaprc.ff12SB
> source leaprc.gaff
> loadamberparams frcmod.ionsjc_tip3p
> UNK = loadmol2 ligand.mol2
> loadamberparams ligand.frcmod
> saveoff UNK ligand.lib
> saveamberparm UNK ligand.prmtop ligand.inpcrd receptor = loadpdb
> protein.pdb saveamberparm receptor receptor.prmtop receptor.inpcrd
> savepdb receptor receptor.pdb saveoff receptor receptor.lib comp =
> combine {receptor UNK} saveamberparm comp complex.prmtop
> complex.inpcrd savepdb comp complex.pdb saveoff comp complex.lib
> addions comp Na+/Cl- 0 solvateoct comp TIP3PBOX 12.0 saveamberparm
> comp complex_solvated.prmtop complex_solvated.inpcrd savepdb comp
> complex_solvated.pdb saveoff comp complex_solvated.lib quit
>
> #MM/GBSA
> Input file for running PB and GB
> &general
> startframe=1500, verbose=1,entropy=1, / &gb
> igb=2, qm_theory = 'PM3', saltcon=0.100 / &decomp
> idecomp=2, dec_verbose= 2
> /
>
> #error
> CalcError: sander failed with prmtop complex.prmtop!
That is not the error -- that's just a message that an error occurred.
The actual error will be printed in one of the temporary mdout files.
Something like _MMPBSA_complex_gb.mdout.0 if you are using only 1 processor.
What is the error message in that file?
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Apr 24 2014 - 08:00:04 PDT
