From owner-nwchem-users@emsl.pnl.gov Fri Jul 6 09:49:11 2007 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.13.8/8.13.8) with ESMTP id l66GnAH3014690 for ; Fri, 6 Jul 2007 09:49:10 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.8/8.13.8/Submit) id l66Gn92l014689 for nwchem-users-outgoing-0915; Fri, 6 Jul 2007 09:49:09 -0700 (PDT) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-Possible-Spoof: True X-IronPort-AV: E=Sophos;i="4.16,509,1175497200"; d="scan'208,217";a="25082894" X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C7BFED.8F4520CE" Subject: RE: [NWCHEM] QM/MM geometry constraints Date: Fri, 6 Jul 2007 09:49:02 -0700 Message-ID: <9EA84B4DE79CD74F89F814624913B70503AA180E@EMAIL01.pnl.gov> In-Reply-To: <59F8E9364A4B184EA893B98611CFC88E01617113@XMAIL.ds.utpa.edu> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: [NWCHEM] QM/MM geometry constraints Thread-index: Ace/RK/2KaZpMPi6R/K69k27HfzfFwAqMNKA References: <59F8E9364A4B184EA893B98611CFC88E01617113@XMAIL.ds.utpa.edu> From: "Valiev, Marat" To: "Mark Cunningham" , X-OriginalArrivalTime: 06 Jul 2007 16:49:03.0330 (UTC) FILETIME=[8F288420:01C7BFED] Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk This is a multi-part message in MIME format. ------_=_NextPart_001_01C7BFED.8F4520CE Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Mark, =20 QM/MM module does not use internal coordinates representation, thus your errors. Also aside the potential use, the actual charmm fragment files have never been tested. I would recommend using AMBER force field. =20 Marat Valiev, Ph.D. Senior Research Scientist Molecular Sciences Software Group (NWChem) marat.valiev@pnl.gov =20 From: owner-nwchem-users@emsl.pnl.gov [mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of Mark Cunningham Sent: Thursday, July 05, 2007 1:40 PM To: nwchem-users@emsl.pnl.gov Subject: [NWCHEM] QM/MM geometry constraints =20 I am trying to use NWChem 5.0 to perform QM/MM calculations but my progress has been hampered by the fact that none of the examples in the distribution actually run. Additionally, it appears that all of the CHARMM fragment files are incorrect. =20 My problem at the moment is to specify a geometry constraint. In an all QM calculation, I can use zcoord to force an atom-atom distance to be some value without having to use an harmonic restraint. In a QM/MM calculation, I tried using=20 the same strategy: after task prepare, I specified: =20 geometry zcoord bond 77 153 3.5 constant torsion 69 71 77 153 178.12 constant end end This results in the following error: User specification of redundant internal variables -------------------------------------------------- i j k l value name frz --- --- --- --- ------------ -------- --- 77 153 3.500000 User001 T 69 71 77 153 178.120000 User002 T Scaling coordinates for geometry "geometry" by 1.889725989 (inverse scale =3D 0.529177249) geom_cart_set: too many centers 0 geometry geom_masses_set: too many centers 0 geometry geom_nucexps_set: too many centers 0 geometry =20 ------------------------------------------------------------------------ geom_input: geom_nucexps_set failed 0 =20 ------------------------------------------------------------------------ =20 ------------------------------------------------------------------------ current input line : 42: end =20 ------------------------------------------------------------------------ I would appreciate any advice. =20 Mark A Cunningham The University of Texas-Pan American =20 ------_=_NextPart_001_01C7BFED.8F4520CE Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Mark,

 

QM/MM module does not use internal coordinates = representation, thus your errors.

Also aside the potential use, the actual charmm fragment = files have never been tested.

I would recommend using AMBER force = field.

 

Marat = Valiev, Ph.D.
Senior Research Scientist
Molecular Sciences Software Group (NWChem)
marat.valiev@pnl.gov

 

From:= owner-nwchem-users@emsl.pnl.gov [mailto:owner-nwchem-users@emsl.pnl.gov] = On Behalf Of Mark Cunningham
Sent: Thursday, July 05, 2007 1:40 PM
To: nwchem-users@emsl.pnl.gov
Subject: [NWCHEM] QM/MM geometry = constraints

 

I am trying to use NWChem 5.0 to perform QM/MM calculations = but my progress

has been hampered by the fact that none of the examples in the = distribution

actually run.  Additionally, it appears that all of the CHARMM fragment = files are

incorrect.

 

My problem at the moment is to specify a geometry constraint.  In an = all QM

calculation, I can use zcoord to force an atom-atom distance to be some = value

without having to use an harmonic restraint.  In a QM/MM calculation, = I tried using

the same strategy: after task prepare, I specified:

 

geometry
   zcoord
      bond 77 153 3.5 constant
      torsion 69 71 77 153 178.12 constant
   end
end

This results in the following error:

User = specification of redundant internal variables
 --------------------------------------------------

   i   j   k   l     value       name   frz
  --- --- --- --- ------------ -------- ---
   77 153           &nbs= p; 3.500000 User001    T
   69  71  77 153   178.120000 User002    T


 Scaling coordinates for geometry "geometry" by  1.889725989
 (inverse scale =3D  0.529177249)

  geom_cart_set: too many centers           =            0 geometry
  geom_masses_set: too many centers           =            0 geometry
  geom_nucexps_set: too many centers           =            0 geometry
 -------------------------------------------------------------------= -----
 geom_input: geom_nucexps_set failed        0
 -------------------------------------------------------------------= -----
 -------------------------------------------------------------------= -----
  current input line :
    42: end
 -------------------------------------------------------------------= -----

I would appreciate any advice.

 

Mark A Cunningham

The University of Texas-Pan American

 

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