AMBER Archive (2006)

Subject: AMBER: Fwd: RESP for deprotonated tyrosine and lysine

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Wed May 24 2006 - 21:57:45 CDT

---------- Forwarded message ----------
From: jitrayut jitonnom <jitrayut.018_at_gmail.com>
Date: 24 ¾.¤. 2006, 17:38 ¹.
Subject: RESP for deprotonated tyrosine and lysine
To: case_at_scripps.edu

Dear Prof.David Case

I want to do the deprotonated tyrosine and lysine (basic form) calculated
using Antechamber with
the RESP charge method based on HF/6-31G* calculations conducted
with Gaussian 98. I have done the guideline that you give in AMBER Archive
(2002) ---
Subject: *Re: RESP tutorial *But I already do for lysine by all steps belows
;

antechamber -i lys.pdb -fi pdb -o lys.gcrt -fo gcrt
g03 <lys.gcrt>tyr_g03.out &
antechamber -i lys_g03.out -fi gout -o g03_lys.prepi -fo prepi -c resp -s 2

and the results were shown belows;

Running: /AMBER/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac -j full

Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C
(4) increase PSCUTOFF in define.h and recompile bondtype.C
    Be cautious, use a large value of PSCUTOFF (>10) will significantly
increase the computer time
Error: cannot run "/AMBER/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0
-o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of
antechamber.c properly, exit

what did I do wrong? I don't know but ,may be, come from the structure I
build or any reasons.

So, please tell me how to do that ,by the way, this attached file should be
useful for you

,Thank you

Ph.D Jitrayut Jitonnom

Chiang Mai University

Thailand

50200


  • chemical/x-pdb attachment: lys.pdb

  • chemical/x-pdb attachment: tyr.pdb
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