AMBER Archive (2007)

Subject: AMBER: MM-GBSA: pairwise decompose energy calculation can't read snapshot_com.all.out

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Sun Jun 03 2007 - 11:08:16 CDT

Dear amber users,

I am facing a problem of calculating decompose energy on pairwise
per-residue by MM-GBSA. By setting DCTYPE = 4, i should get the pair
decompositon energy. But it seems that the process fail and stop reading the
snapshot_com.all.out file as shown below. By the way, i have recently
finished on decompose per residue calculation but in this case i can't
obtained the results which i think it could work too.

The bottom line of log file.
=>> 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: 1 - 7
=>> Reading files
    Reading snapshot_com.all.out <STOP HERE>

Also, I have checked the size of snapshot_com.all.out and it has a large
file (~ 1GB). So, it is possible that the file is too large to read and then
stop reading. If it so how can i solve this problem. The second question
is " Can the decompose energy calculated by MM-PBSA ?".

Any comment would be great.

For more details for my input are here.

PREFIX snapshot
PATH ../01_generate_snapshot/
#
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 4
#
COMREC 1-230
COMLIG 231-237
COMPRI 1-237
RECRES 1-230
RECPRI 1-230
RECMAP 1-230
LIGRES 1-7
LIGPRI 1-7
LIGMAP 1-7
@MM
DIELC 1.0
@GB
IGB 2
GBSA 2
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00

Best regards,

Jitrayut

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