AMBER Archive (2009)

Subject: [AMBER] MMPBSA extract coordinate

From: vijayaraj_at_clri.res.in
Date: Fri May 22 2009 - 13:00:57 CDT

Hi,

 I am trying to extract coordintes from traj to carry out mmpbsa
calculation using amber9. My input traj has more than one receptor
molecules and i need to club all the receptor molecules as one unit and
its binding energy with one ligand. when i run the extract_coordinate, i
am getting the follwing error message,

forrtl: severe (64): input conversion error, unit 5, file stdin
Image PC Routine Line Source
make_crd_hg 0000000000475D0E Unknown Unknown Unknown
make_crd_hg 0000000000474F0A Unknown Unknown Unknown
make_crd_hg 000000000043843E Unknown Unknown Unknown
make_crd_hg 000000000040D3EA Unknown Unknown Unknown
make_crd_hg 000000000040CA06 Unknown Unknown Unknown
make_crd_hg 0000000000420E19 Unknown Unknown Unknown
make_crd_hg 00000000004073BF Unknown Unknown Unknown
make_crd_hg 0000000000402F22 Unknown Unknown Unknown
libc.so.6 000000343181C3FB Unknown Unknown Unknown
make_crd_hg 0000000000402E6A Unknown Unknown Unknown

here is my input,

@GENERAL
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
GC 1
AS 0
DC 0
MM 0
GB 0
PB 0
MS 0
NM 0
@MAKECRD
BOX YES
NTOTAL 13876
NSTART 3500
NSTOP 4000
NFREQ 100
NUMBER_LIG_GROUPS 1
LSTART 1
LSTOP 80
NUMBER_REC_GROUPS 7
LSTART 81
LSTOP 160
LSTART 161
LSTOP 240
LSTART 241
LSTOP 320
LSTART 321
LSTOP 400
LSTART 401
LSTOP 480
LSTART 481
LSTOP 560
LSTART 561
LSTOP 640
@TRAJECTORY
TRAJECTORY ./pro.mdcrd

could any one give me a solution to solve this.

vijay.

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