Hi Jitrayut,
it seems I had the same problem. Probably if you change the following
thing you'll succeed if you don't have other error sources:
jitrayut jitonnom wrote:
> Dear amber users,
>
> I have problem on running mmpbsa using AMBER9 to obtain the decompose
> energy. After i extracted 100 snapshots and then performed the
> decompose_energy.in as show below; i found the error during the mmpbsa
> process like this
>
> " Missing values for MM BGAS "
>
> When i check the end of the log file of this process, it stop at line
> below;
>
> =>> Doing statistics
> =>> Values of global variables
> TEMP = 300
> R = 8.314
> gammaP = 0.00542
> betaP = 0.92
> gammaG = 0.0072
> betaG = 0.00
> =>> Reading input
> =>> Reordering files
> Final order:
> 1. snapshot_com.all.out: 1 - 237
> 2. snapshot_rec.all.out: 1 - 230
> 3. snapshot_lig.all.out: 231 - 237
> =>> Reading files
> Reading snapshot_com.all.out
> Reading snapshot_rec.all.out
> Checking CALC
> Reading snapshot_lig.all.out
>
> For the decompose_energy.in are following;
>
> .GENERAL
> PREFIX snapshot
> PATH ./
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ./enz-lig.top
> RECPT ./enz.top
> LIGPT ./lig.top
> #
> GC 0
> AS 0
> DC 1
> #
> MM 1
> GB 1
> PB 0
> MS 0
> #
> NM 0
> ############################################################################
>
> .DECOMP
> DCTYPE 2
> #
> COMREC 1-230
> COMLIG 231-237
> COMPRI 1-237
> RECRES 1-230
> RECPRI 1-230
> RECMAP 1-230
> LIGRES 231-237
> LIGPRI 231-237
Should be instead:
LIGRES 1-7
LIGPRI 1-7
because in your topology file for the ligand, which you should have
created separately, there are no numbers 231-237, so the program doesn't
find them.
Best regards,
Sergey
> LIGMAP 231-237
> ############################################################################
> .MM
> DIELC 1.0
> ############################################################################
> .GB
> IGB 2
> GBSA 2
> SALTCON 0.00
> EXTDIEL 80.0
> INTDIEL 1.0
> #
> SURFTEN 0.0072
> SURFOFF 0.00
>
>
> So, any suggestions will be grate.
>
> Thank you in advance,
>
> Jitrayut Jitonnom
>
>
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Received on Wed Apr 25 2007 - 06:07:19 PDT
