AMBER Archive (2005)

Subject: AMBER: about antechamber(amber8)

From: linfu (linfu3200_at_mail.sioc.ac.cn)
Date: Thu Dec 15 2005 - 01:51:16 CST

amberDear Amber communinty!

Recently I encounter a warning below when i use antechamber(amber8) in the SGI unix.
and antechamber produces the file ligand.prep,however, i am not sure whether ligand.prep
is right or not because of the warnings.

Another question is about energy. I use explicit water model to do MD. After MD, in the file md.out, does the totoal energy include water-water electrostatic interaction and
water-water vdw interaction?
Could you help me to figure out the solution and how to reallocate the memory!

Thank you very much:)

                          for the second problem
______________________________________________________________________________
      A V E R A G E S O V E R 20000 S T E P S

 NSTEP = 20000 TIME(PS) = 20.000 TEMP(K) = 209.59 PRESS = -74.4
 Etot = -10568.2571 EKtot = 2496.4609 EPtot = -13064.7181
 BOND = 1233.7483 ANGLE = 48.1155 DIHED = 114.3170
 1-4 NB = 30.8466 1-4 EEL = 369.1724 VDWAALS = 2585.6321
 EELEC = -17465.3018 EHBOND = 0.0000 RESTRAINT = 18.7517
 EAMBER (non-restraint) = -13083.4698
 EKCMT = 1178.7489 VIRIAL = 1260.0694 VOLUME = 42488.7791
                                                Density = 0.9482
 Ewald error estimate: 0.1529E-03
 ------------------------------------------------------------------------------

                             for the first problem

compchem 39% antechamber -i ligand.out -fi gout -o ligand.prep -fo prepi -c resp

The number of the ESP exceeds the MAXESP(20000),extend the size and reallocate the memory
The number of the ESP exceeds the MAXESP(30000),extend the size and reallocate the memory

The number of the path atoms exceeds MAXPATHATOMNUM(10000) for atom[11],extend the size and reallocate the memory
   ------------------------------------
   ------------------------------------
and reallocate the memory
The number of the path atoms exceeds MAXPATHATOMNUM(10000) for atom[5 ],extend the size and reallocate the memory

Amber8 Module: resp
Amber8 Module: resp

compchem 42% ls
ANTECHAMBER.ESP ANTECHAMBER_PREP.AC ANTECHAMBER_RESP1.OUT NEWPDB.PDB ligand.out
ANTECHAMBER_AC.AC ANTECHAMBER_PREP.AC0 ANTECHAMBER_RESP2.IN PREP.INF ligand.prep
ANTECHAMBER_AC.AC0 ANTECHAMBER_RESP.AC ANTECHAMBER_RESP2.OUT QOUT punch
ANTECHAMBER_BOND_TYPE.AC ANTECHAMBER_RESP1.IN ATOMTYPE.INF esout qout
_____________________________________________________________________________
                                 

　　　　　　　　linfu
　　　　　　　　linfu3200_at_mail.sioc.ac.cn
　　　　　　　　　　
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