AMBER Archive (2006)

Subject: AMBER: error about the number of snapshots

From: AYTUG TUNCEL (ATUNCEL_at_ku.edu.tr)
Date: Tue Nov 07 2006 - 15:11:24 CST

Dear amber users,

I have a 5 ns .crdbox formated simulation trajectory. The system is composed of two protein chains (rec = 6903, lig = 6873 atoms, and totaly 103072 atoms with water). Time interval between two consequtive frames is 5 ps which means 1000 frames overall. Number of snapshots I want to take is 1000 (which I guess the max number in my case) using mm_pbsa method, but when it comes to snapshot 355 it gives the following error;

forrtl: severe (64): input conversion error, unit 5, file stdin
Image PC Routine Line Source
make_crd_hg 080978A2 Unknown Unknown Unknown
make_crd_hg 08095F75 Unknown Unknown Unknown
make_crd_hg 080765CD Unknown Unknown Unknown
make_crd_hg 08051D1A Unknown Unknown Unknown
make_crd_hg 08051A4A Unknown Unknown Unknown
make_crd_hg 080619A2 Unknown Unknown Unknown
make_crd_hg 0804D921 Unknown Unknown Unknown
make_crd_hg 08049C45 Unknown Unknown Unknown
libc.so.6 B7CA6EC2 Unknown Unknown Unknown
make_crd_hg 08049B71 Unknown Unknown Unknown
    Close TO failed: 16384/

I tried to obtain less number of snapshots, but it gives me the same error even when I try only 100 snapshots. One thing I want to indicate is that I did the simulatin with NAMD and joined the .dcd formatted trajectory files(totaly it makes a 850 MB file) with catdcd4.0 program, which can also convert the the dcd format to crdbox format.

Does anybody have any suggestions about the problem?
Thanks in advance.

Aytug Tuncel
e_crd_hg 08051D1A Unknown Unknown Unknown
make_crd_hg 08051A4A Unknown Unknown Unknown
make_crd_hg

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