AMBER Archive (2007)

Subject: Re: AMBER: Non-standard amino acid residue

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Wed Jul 18 2007 - 09:19:42 CDT

Hello Francois,

FyD wrote:
> Quoting Sergey Samsonov <sergeys_at_biotec.tu-dresden.de>:
>
>> That's what I mean exactly, to calculate the charges in AM1-BCC is not
>> the correct way to proceed with non-standard amino acid residues since
>> even the charges for the atoms of the same standard residue in the same
>> conformation will be really different if calculate in RESP and in
>> AM1-BCC, that is quite logical since the methods are principally
>> different.
>
> Personnally, I work with RESP charges and even with this approach
> there are many pitfalls... Since it is already difficult to reproduce
> published RESP charge values, I am not surprised the differences are
> even higher with AM1-BCC.
>
>> Trying RESP I faced another problem (it was already mentioned in the
>> mailing list but no really helpful answer was given,
>> http://structbio.vanderbilt.edu/archives/amber-archive/2005/0324.php).
>> When I try to produce the prepin file using antechamber by:
>>
>> antechamber -i name.log -fi gout -o name.prepi -fo prepi -c resp -s 2
>> I receive the error:
>> Amber8 Module: resp
>> Unit 10 Error on OPEN: ANTECHAMBER.ESP
>> Amber8 Module: resp
>> Unit 3 Error on OPEN: qout
>> Cannot open charge file QOUT , exit
>>
>> It seems that I should create ANTECHAMBER.ESP first? How can I deal
>> with that?
>
> Sorry, I use R.E.D. with
> multi-molecules/multi-conformations/multi-orientations RESP fit. This
> allows to generate (i)multi-orientations: highly reproducible RESP
> charge values, (ii)multi-conformations: general/high quality charge
> values required in MD simulation and (iii)multi-molecules: to generate
> charge values for any types of molecular fragments.

I just tried to follow the examples with already prepared files from the
web tutorial which I have all in the same directory.
After I start perl RED-vIII.pl

---------------------------
                      * Welcome to R.E.D. III *
                         RESP ESP charge Derive
                  http://q4md-forcefieldtools.org/RED/

                         CHARGE TYPE = RESP-A1
                      ---------------------------

        ERROR: The initial P2N file can not be found

Do you think there could be any problems with RED because I use AMBER8.0
and not AMBER9.0 version?

At the same time when I do test/antechamper/Run_tp_resp I get this:

Running: $AMBERHOME/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac -j full
Running: $AMBERHOME/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
Running: $AMBERHOME/exe/espgen -o ANTECHAMBER.ESP -i tp.log
Running: $AMBERHOME/exe/respgen -i ANTECHAMBER_RESP.AC -o
ANTECHAMBER_RESP1.IN -f resp1
Running: $AMBERHOME/exe/respgen -i ANTECHAMBER_RESP.AC -o
ANTECHAMBER_RESP2.IN -f resp2
Running: resp -O -i ANTECHAMBER_RESP1.IN -o ANTECHAMBER_RESP1.OUT -e
ANTECHAMBER.ESP -t qout
Amber8 Module: resp
forrtl: severe (24): end-of-file during read, unit 5, file
/home/bioinfp/sergeys/AmberMy/RESP/Test/ANTECHAMBER_RESP1.IN
Image PC Routine Line Source
resp 080A5A5A Unknown Unknown Unknown
resp 080A48B9 Unknown Unknown Unknown
resp 08085E45 Unknown Unknown Unknown
resp 0805C58E Unknown Unknown Unknown
resp 0805C2BE Unknown Unknown Unknown
resp 0806A01C Unknown Unknown Unknown
resp 08049F79 Unknown Unknown Unknown
resp 08049DA9 Unknown Unknown Unknown
resp 08049C35 Unknown Unknown Unknown
libc.so.6 003A0DE3 Unknown Unknown Unknown
resp 08049B71 Unknown Unknown Unknown
resp -O -i ANTECHAMBER_RESP2.IN -o ANTECHAMBER_RESP2.OUT -e
ANTECHAMBER.ESP -q qout -t QOUT

Sorry for the troubles and thank you very much!

Sergey
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