AMBER Archive (2004)

Subject: AMBER: What happen when sander reads charge increments from cpin file?

From: Yongzhi Chen (yongzhi_mms_at_yahoo.com)
Date: Wed Jul 21 2004 - 15:24:51 CDT

Dear Amber users/developers,

I met a very strange problem in constant pH
calculation of Amber8.

According to the instruction in manual, I added the
necessary command line flags to sander to support
constant pH operation. When I check the output file to
get progress information, I found that output was stop
at the line "reading charge increments from
file: 3BTA_PH.cpin". I monitored the nodes and found
that each processor was "busy". I waited for a long
time but got no result so I had to kill this job. From
the output file for this job, I got these messages:

forrtl: severe (18): too many values for NAMELIST
variable, unit 18,
file /nfs/s09r1p1/yonchen/3BTA_PH/3BTA_PH.cpin
Image PC Routine Line
     Source

sander 081B9949 Unknown
Unknown Unknown
sander 08181BB3 Unknown
Unknown Unknown
sander 0818205A Unknown
Unknown Unknown
sander 0819C33A Unknown
Unknown Unknown
sander 080B1D11 Unknown
Unknown Unknown
sander 080B8640 Unknown
Unknown Unknown
sander 0807D0F2 Unknown
Unknown Unknown
sander 0807BBB9 Unknown
Unknown Unknown
sander 0804B548 Unknown
Unknown Unknown
Unknown 2ABA9A67 Unknown
Unknown Unknown
sander 0804B401 Unknown
Unknown Unknown

I used the same method and configure file to operate a
protein from the tutorial, wt1mg.pdb, whose size was
about 1/10 of mine. Everything is OK. I compared these
two sets very carefully but got no hints. Is a 60K
cpin file too big for the sander?

Thank you for your help!

Best,
Yongzhi

        
                
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