From owner-chemistry@ccl.net Tue Sep 29 05:56:00 2009 From: "Van Dam, Huub (STFC,DL,CSE) huub.van-dam ~~ stfc.ac.uk" To: CCL Subject: CCL:G: Software for Intermolecular Forces Calculation Message-Id: <-40373-090929055153-14066-V8IESCM5nmz4IKvw9Qi3Bw,+,server.ccl.net> X-Original-From: "Van Dam, Huub (STFC,DL,CSE)" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01CA40E1.5AEFA78F" Date: Tue, 29 Sep 2009 09:46:35 +0100 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Huub (STFC,DL,CSE)" [huub.van-dam_-_stfc.ac.uk] This is a multi-part message in MIME format. ------_=_NextPart_001_01CA40E1.5AEFA78F Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear Yangsoo, =20 A code that can do what you need is DMAREL. This code is designed for periodic systems but could be made to work in a super cell context (see the comments from Bill Smith below). At present DMAREL and it is more up to date version DMACRYS are used for example by Prof. Sally L. Price at University College London to predict polymorphs of organic molecules (http://www.chem.ucl.ac.uk/cposs/briefoverview.html). I hope this helps. =20 Best wishes, =20 Huub =20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D Huub van Dam (huub.van-dam]=[stfc.ac.uk, +44-1925-603933) =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D > From: Smith, Bill (STFC,DL,CSE)=20 Sent: 29 September 2009 09:19 To: Van Dam, Huub (STFC,DL,CSE) Subject: RE: G: Software for Intermolecular Forces Calculation =20 Hi Huub, =20 I've been away, so sorry for the late reply. DMAREL is certainly a possibility for this, though it is designed to work with periodic systems, which may be a problem for this user. Also I'm not sure it will print out forces (though it MUST calculate first derivatives internally so it could be added). It will handle dipoles, charges etc, though again it is assumed this is in a periodic system and it will be necessary to set the Ewald convergence parameter to zero. Should be possible though. =20 DMAREL can be obtained via CCP5 (www.ccp5.ac.uk). There is a more up-to-date version of DMAREL called DMACRYS available from (www.cposs.org.uk ). =20 Bill =20 > From: Van Dam, Huub (STFC,DL,CSE)=20 Sent: 22 September 2009 16:11 To: Smith, W (Bill) Subject: FW: G: Software for Intermolecular Forces Calculation =20 Hi Bill, I wondered if DMAREL could be used to answer the type of question considered. Could you let me know, please? =20 Huub =20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D Huub van Dam (huub.van-dam]=[stfc.ac.uk, +44-1925-603933) =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D > From: owner-chemistry+huub.van-dam=3D=3Dstfc.ac.uk]=[ccl.net [mailto:owner-chemistry+huub.van-dam=3D=3Dstfc.ac.uk]=[ccl.net] On Behalf = Of Yangsoo Kim vsmember()gmail.com Sent: 22 September 2009 14:36 To: Van Dam, Huub (STFC,DL,CSE) Subject: CCL:G: Software for Intermolecular Forces Calculation =20 Dear All, =20 I'm wondering if anyone of you knows any software (commercial or free) that can calculate the values related to intermolecular forces (many body interactions) such as van der Waals forces, dipole-dipole interactions, and hydrogen bonding for a pure compound, under the conditions that only the 3D-structure of the single molecule is available, which is determined from quantum optimization calculations by GAMESS or Gaussian. =20 Any suggestion or advice is greatly appreciated. =20 Many thanks in advance, =20 Yangsoo Kim =20 =20 -- =0AScanned by iCritical.=0A ------_=_NextPart_001_01CA40E1.5AEFA78F Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear Yangsoo,

 

A code that can do what you need is DMAREL. This code is designed for periodic systems but could be made to work in a super cell = context (see the comments from Bill Smith below). At present DMAREL and it is = more up to date version DMACRYS are used for example by Prof. Sally L. Price at = University College London to predict polymorphs of organic molecules (http://www.ch= em.ucl.ac.uk/cposs/briefoverview.html). I hope this helps.

 

Best wishes,

 

      Huub

 

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Huub van Dam (huub.van-dam]=[stfc.ac.uk, +44-1925-603933)
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D

From: Smith, Bill = (STFC,DL,CSE)
Sent: 29 September 2009 09:19
To: Van Dam, Huub (STFC,DL,CSE)
Subject: RE: G: Software for Intermolecular Forces = Calculation

 

Hi Huub,

 

I’ve been away, so sorry for the late reply.  = DMAREL is certainly a possibility for this, though it is designed to work with periodic systems, which may be a problem for this user. Also I’m = not sure it will print out forces (though it MUST calculate first derivatives = internally so it could be added). It will handle dipoles, charges etc, though again = it is assumed this is in a periodic system and it will be necessary to  = set the Ewald convergence parameter to zero. Should be possible = though.

 

DMAREL can be obtained via CCP5 (www.ccp5.ac.uk). There is a more up-to-date version of DMAREL called DMACRYS available = > from (www.cposs.org.uk = ).

 

Bill

 

From: Van Dam, Huub (STFC,DL,CSE)
Sent: 22 September 2009 16:11
To: Smith, W (Bill)
Subject: FW: G: Software for Intermolecular Forces = Calculation

 

Hi Bill,

I wondered if DMAREL could be used to answer the type of question considered. Could you let me know, = please?

 

Huub

 

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Huub van Dam (huub.van-dam]=[stfc.ac.uk, +44-1925-603933)
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D

From: owner-chemistry+huub.van-dam=3D=3Dstfc.ac.uk]=[ccl.net [mailto:owner-chemistry+huub.van-dam=3D=3Dstfc.ac.uk]=[ccl.net] On = Behalf Of Yangsoo Kim vsmember()gmail.com
Sent: 22 September 2009 14:36
To: Van Dam, Huub (STFC,DL,CSE)
Subject: CCL:G: Software for Intermolecular Forces = Calculation

 

Dear = All,

 

I’m wondering if anyone of you = knows any software (commercial or free) that can calculate the values related to intermolecular forces (many body interactions) such as van der Waals = forces, dipole-dipole interactions, and hydrogen bonding for a pure compound, = under the conditions that only the 3D-structure of the single molecule is = available, which is determined from quantum optimization calculations by GAMESS or Gaussian.

 

Any suggestion or advice is = greatly appreciated.

 

Many thanks in = advance,

 

Yangsoo = Kim

 

 


=

-- =0A
Scanned by iCritical.=0A


= ------_=_NextPart_001_01CA40E1.5AEFA78F-- From owner-chemistry@ccl.net Tue Sep 29 09:30:00 2009 From: "Jenny U alchjhy()hotmail.com" To: CCL Subject: CCL: Qustions about docking(metalloprotein) with FlexX Message-Id: <-40374-090929092852-25505-ftUXhnqMREizk8CYHFH56Q++server.ccl.net> X-Original-From: "Jenny U" Date: Tue, 29 Sep 2009 09:28:48 -0400 Sent to CCL by: "Jenny U" [alchjhy _ hotmail.com] i wanna use FlexX to dock metalloprotein. I added extra metal to target protein, FlexX does recognize it, but cannot give right coordination for extra metal. In detail, when i define receptor, at the metal define step, FlexX doesn't give statistical coordination, and i cannot select right coordination because it doesn't work. how can i solve it? plz help me. name : Jenny U email : alchjhy{}hotmail.com From owner-chemistry@ccl.net Tue Sep 29 11:20:00 2009 From: "Pablo Englebienne p.englebienne-#-tue.nl" To: CCL Subject: CCL: Software for polymer MD simulations Message-Id: <-40375-090929110012-26244-CMGcOcsWundp9yrs2HKt4g_._server.ccl.net> X-Original-From: Pablo Englebienne Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Tue, 29 Sep 2009 16:10:04 +0200 Mime-Version: 1.0 (Apple Message framework v935.3) Sent to CCL by: Pablo Englebienne [p.englebienne(!)tue.nl] Hi all, As a recent mover from the field of biomolecular to materials simulations, I would like to request your input to ease this transition. I am looking to perform atomistic simulations (MD, MC) of synthetic polymers and co-polymers. Reviewing the literature, it is hard to decide a simulation engine/force field combination. I am currently looking at GROMACS, NAMD, LAMMPS and DL_POLY, for reasons of available local expertise (GROMACS, NAMD) and apparent suitability for materials (LAMMPS, DL_POLY). There is not a definite choice, however. I would appreciate receiving comments/suggestions about these options, as well as others I might be overlooking. I am also looking for a program to construct initial coordinates of a random copolymer, if there was something like that ever coded. Optimally, I would like to be able to have structures of monomers (in some format), their relative ratio in the polymer and the chain length as input, and have coordinates (in some format) for the polymer as output. I am willing to wrap something together myself, but I was curious if there was a tool out there to do it. Kind regards, Pablo -- Pablo Englebienne, PhD Institute of Complex Molecular Systems (ICMS) Eindhoven Univeristy of Technology, TU/e PO Box 513, HG -1.26 5600 MB Eindhoven, The Netherlands Tel +31 40 247 5349 From owner-chemistry@ccl.net Tue Sep 29 14:49:01 2009 From: "Jose M Orts jm.orts]*[ua.es" To: CCL Subject: CCL: external electric field in VASP 4.6 Message-Id: <-40376-090929130412-31952-wRVe8VpVubvLUsgdRUDTVw-.-server.ccl.net> X-Original-From: "Jose M Orts" Date: Tue, 29 Sep 2009 13:04:08 -0400 Sent to CCL by: "Jose M Orts" [jm.orts:ua.es] I am interested in making calculations in VASP 4.6, applying an external electric field. It seems that the code allows this, but the relevant keywords (tags) to be included in the INCAR file are not detailed in the VASP manual. Some posts seem to exist at VASP forum,(related to EFIELD) but the text of these seems to be unreachable (VASP forum not functioning, or discontinued?). I will appreciate any help on this point. JMOrts Departamento de Qumica Fsica Universidad de Alicante From owner-chemistry@ccl.net Tue Sep 29 21:41:01 2009 From: "jmarta(!)chem.meisei-u.ac.jp" To: CCL Subject: CCL:G: Gaussian calculation problem Message-Id: <-40377-090929011411-10598-KVP31wg1rEHoz9JSuRSxbg{=}server.ccl.net> X-Original-From: Content-Transfer-Encoding: QUOTED-PRINTABLE Content-Type: text/plain; charset=UTF-8 Date: Tue, 29 Sep 2009 13:37:45 +0900 (JST) MIME-Version: 1.0 Sent to CCL by: [jmarta^chem.meisei-u.ac.jp] Dear Madame/Sir, I use the windows based Gaussian (Gaussian03W) and I would like to make calculation on a molecule at DFT level, using Bader's atoms in molecules (AIM) theory.=20 As I know AIM does not with core potential basis sets. So I used an all electron basis set for the whole Cisplatin molecule= . I checked Gaussian 03 Manual and I found only one basis set UGBS(1,2,3)P = which is defined also on Pt and does not contain ECP. I tried the caluclati= on using UGBS bais set for each element (H, N, Cl and Pt). That is true tha= t this UGBS is written in the Gaussian 03 Manual book, but it is not in the= program (in the GaussView when I want to choose the theory level and basis= set, this UGBS can not be found there as a option, but I typed this).=20 So the route section was: # opt freq b3lyp/ugbs geom=3Dconnectivity aim=3Dall and the Gaussian started but 8 minutes later it stoped and the next error m= essage was appeared: No special actions if energy rises. Defaulting to unpruned grid for atomic number 78. Spurious integrated density or basis function: NE=3D 132 NElCor=3D 0 El error=3D2.40D-04 rel=3D1.82D-06 Tolerance=3D1= ..00D-03 Shell 1 absolute error=3D1.00D+00 Tolerance=3D1.20D-0= 2 Shell 6 signed error=3D7.38D-01 Tolerance=3D1.00D-0= 1 Inaccurate quadrature in CalDSu. The absolute error is bigger than the tolerance value what I do not know ho= w to decrease. I also tried use UGBS1P basis set but this calculation requi= res higher memory what I have on the computer. Would you be so nice to tell me what can be the problem and how I can solve it? Thank you very much in advance. Sincerely, Dr. Marta JUHASZ Meisei University Department of Chemistry JAPAN