AMBER Archive (2007)

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

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Thu Jul 19 2007 - 04:45:52 CDT

Hello Francois,

FyD wrote:
> R.E.D. needs Mol_red$n.p2n files to run...
>
> For instance:
> - If $n = 1 (This is a single molecule fitting approach), you only
> need to provide Mol_red1.p2n (the name being fixed)...
> - If $n = 3 (This is a three molecule charge fitting approach), you
> need to provide three p2n files: Mol_red1.p2n, Mol_red2.p2n and
> Mol_red3.p2n.
> - Now, if you provide Mol_red1.p2n, Mol_red2.p2n and Mol_red4.p2n,
> R.E.D. will only use the 2 first p2n files since you have a hole in
> the list of p2n files.
Thank you. It was the reason for this error. Now the file is found but I
get other errors.
In case $OPT_Calc ="On" I receive:

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

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

  
===========================================================================
  ======================= Single molecule
===========================
         The molecule TITLE is "MOLECULE"
                The TOTAL CHARGE value of the molecule is "0"
              The SPIN MULTIPLICITY value of the molecule is "1"
  
===========================================================================

                     * 1 conformation(s) selected *

                               WARNING:
                  A 2nd column of atom names is detected
        This 2nd column will be used in the PDB (& Tripos) file(s)

                               WARNING:
         No three atom based re-orientation found in the P2N file
     Re-orientation will be done according to the GAMESS Algorithm!

                        * Selected QM Software *
                                GAMESS

                         * Software checking *
           rungms
[ OK ]
           gamess.01.x
[ OK ]
           ddikick.x
[ OK ]
           resp
[ OK ]

                ERROR: The Scratch directory is NOT empty

In case $OPT_Calc ="On" I receive:
 ---------------------------
                      * Welcome to R.E.D. III *
                         RESP ESP charge Derive
                  http://q4md-forcefieldtools.org/RED/

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

  
===========================================================================
  ======================= Single molecule
===========================
         The molecule TITLE is "MOLECULE"
                The TOTAL CHARGE value of the molecule is "0"
              The SPIN MULTIPLICITY value of the molecule is "1"
  
===========================================================================

        ERROR: The optimization OUTPUT can not be found

I tried both own examples and the ones from Tutorial. It seems like I
should probably change the names of some files but I cannot understand
which ones.

>
>> 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, I do not know very well antechamber. Can you execute resp in a
> standalone way ? i.e. "without antechamber" using the command just
> above printed by antechamber:
>
> resp -O -i ANTECHAMBER_RESP2.IN -o ANTECHAMBER_RESP2.OUT -e
> ANTECHAMBER.ESP -q qout -t QOUT
The problem is that I don't have .IN files created.

Thank you very much in advance once more!

Sergey

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu