For the antechamber question, those warning message is just for information purpose and your ligand.prep file should be OK. Please try to use the latest antechamber package (v1.23) from the antechamber home page.
Regards
Junmei
==================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals Inc.
7000 Fannin, Houston TX 77030
Tel: 713-578-6649
Email: jwang.encysive.com
http://amber.scripps.edu/antechamber/antechamber.html
==================================================
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of linfu
Sent: Thursday, December 15, 2005 1:51 AM
To: amber
Subject: AMBER: about antechamber(amber8)
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.mail.sioc.ac.cn
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Received on Thu Dec 15 2005 - 16:53:01 PST
