Dear Amber users,
I have AMBER 10 and have been running calculation with the MM-PBSA, there is no problem with extract_coords.mmpbsa, with binding_energy.mmpbsa , first i have this error message
Calculating energy / entropy contributions
Calc contrib for ./snapshot_com.crd.1
Calc MM/GB/SAS
Minimize structure
sander -O -i sanmin_com.in -o sanmin_com.1.out -c ./snapshot_com.crd.1 -p ./mm.prmtop -r sanmin_com.1.restrt not running properly
The sanmin_com.1.out look:
NTXO ( 0) must be 1.
(ntx0=0 is no longer supported)
I followed
the solution posted here
http://structbio.vanderbilt.edu/archives/amber-archive/2008/3564.php, now i have this problem:
Calculating energy / entropy contributions
Calc contrib for ./snapshot_com.crd.1
Calc MM/GB/SAS
Minimize structure
Calc entropy
forrtl: severe (39): error during read, unit 53, file /home/mohamed/lens/charge/rlmod/OUTDM/DM/1-2/mmpbsa2/sanmin_com.1.restrt
Image PC Routine Line Source
nmode 083C0BD1 Unknown Unknown Unknown
nmode 083C0155 Unknown Unknown Unknown
nmode 083806BE Unknown Unknown Unknown
nmode 08349E36 Unknown Unknown Unknown
nmode 08349AD1 Unknown Unknown Unknown
nmode 083580B3 Unknown Unknown Unknown
nmode 08055911 Unknown Unknown Unknown
nmode 0804947E Unknown Unknown Unknown
nmode 08048245 Unknown Unknown Unknown
nmode 083CBB7B Unknown Unknown Unknown
nmode 08048151 Unknown Unknown Unknown
AMBERHOME/exe/nmode -O -i nmode_com.in -o nmode_com.1.out -c sanmin_com.1.restrt -p ./mm.prmtop not running properly
the sanmin_com.1.out look:
*******************************************************
Initiate the NMODE module of AMBER 8
*******************************************************
File generated by mm_pbsa.pl
ntrun maxcyc ibelly drms
1 100 0 0.10E+01
rcut scnb scee dielc idiel
99.00000 2.00000 1.20000 4.00000 0
nsave dfpred bdwnhl smx emx alpha ndiag
20 0.01000 0.10000 0.08000 0.30000 0.80000 10
ipol = 0
i3bod = 0
nvect = 0
Binary format used for input coords.
| New format PARM file being parsed.
| Version = 1.000 Date = 03/26/09 Time = 17:50:22
PARM file has the title:
BCD
Total memory required : 770778 real words
Total memory required : 48217 integer words
Total memory required : 718 4-character words
Maximum nonbond pairs 27965
Duplicated 0 dihedrals
Duplicated 0 dihedrals
Thanks in advance for any help I receive
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Received on Wed May 20 2009 - 12:22:28 PDT
