From chemistry-request@ccl.net Fri Mar  4 06:40:14 2005
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Date: Fri, 04 Mar 2005 11:49:34 +0100
From: "Mgr. Lubos Vrbka" <lubos.vrbka=at=uochb.cas.cz>
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Subject: CCL: addiong ions to simulation box
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Hello everybody:

Is anyone aware of software allowing replacing waters in the simulations 
cell (protein + water box) by small molecules? "Automatic" solution is 
preferred, since I need to put many molecules to the solution.

Any help is highly appreciated. With best regards,
Lubos

-- 
.....................................................
Mgr. Lubos Vrbka

Center for Biomolecules and Complex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
.....................................................

From chemistry-request@ccl.net Fri Mar  4 07:51:05 2005
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Cc: chemistry<<at>>ccl.net
Subject: Re: CCL:addiong ions to simulation box
References: <42283D3E.7050509<<at>>uochb.cas.cz> <1109938027.7750.348.camel<<at>>drugs.ucd.ie>
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> I think you should say what software you are using...
mostly i use amber, however anything capable of working with PDB files 
would do the job...

regards,
lubos


-- 
.....................................................
Mgr. Lubos Vrbka

Center for Biomolecules and Complex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
.....................................................

From chemistry-request@ccl.net Fri Mar  4 07:52:38 2005
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Subject: Re: CCL:adding molecules to simulation box
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> Hi,
> You can do that with VMD. At the VMD console, type:
> package require autoionize
> autoionize
i am sorry, i probably wasn't clear enough - i need to add molecules and 
molecular ions to the box; from what i know, autoionize is capable of 
adding atomic ions only...

regards,
lubos


-- 
.....................................................
Mgr. Lubos Vrbka

Center for Biomolecules and Complex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
.....................................................


From chemistry-request@ccl.net Thu Mar  3 20:54:27 2005
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Date: Thu, 3 Mar 2005 19:58:43 -0500 (EST)
From: Connie Chang <cc236 * ccmr.cornell.edu>
To: chemistry * ccl.net
Subject: Frequency Job ends in error
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Hi,

I've been doing a frequency job with Gaussian 2003 using LINDA on 3
processors.  It seems to go smoothly, going through the passes fine:

 G2DrvN: will do   15 centers at a time, making   10 passes doing
MaxLOS=1.
 FoFDir/FoFCou used for L=0 through L=1.
          Differentiating once with respect to electric field.
                with respect to dipole field.
          Differentiating once with respect to nuclear coordinates.
 Integrals replicated using symmetry in FoFDir.
 MinBra= 0 MaxBra= 1 Meth= 1.
 IRaf=       0 NMat=  38 IRICut=      38 DoRegI=T DoRafI=T ISym2E= 2
JSym2E=2.
 Raff turned off since only 25.39% of shell-pairs survive.
          There are 114 degrees of freedom in the 1st order CPHF.
   114 vectors were produced by pass  0.
 AX will form  38 AO Fock derivatives at one time.
   114 vectors were produced by pass  1.
   114 vectors were produced by pass  2.
   114 vectors were produced by pass  3.
   114 vectors were produced by pass  4.
   114 vectors were produced by pass  5.
   114 vectors were produced by pass  6.
    66 vectors were produced by pass  7.
     9 vectors were produced by pass  8.
     3 vectors were produced by pass  9.
     3 vectors were produced by pass 10.
     3 vectors were produced by pass 11.
     3 vectors were produced by pass 12.
 Inv2:  IOpt= 1 Iter= 1 AM= 5.82D-15 Conv= 1.00D-12.
 Inverted reduced A of dimension  885 with in-core refinement.
 Isotropic polarizability for W=    0.000000      987.15 Bohr**3.
 End of Minotr Frequency-dependent properties file   721 does not exist.

But then it ends in error before outputing the frequencies while it's
calculating the moments and polarizability as below:

Dipole moment (field-independent basis, Debye):
    X=     0.0000    Y=     0.0000    Z=     0.0000  Tot=     0.0000
 Quadrupole moment (field-independent basis, Debye-Ang):
   XX=  -707.9020   YY=  -713.3250   ZZ=  -708.3146
   XY=     4.8215   XZ=     0.0000   YZ=     0.0000
 Traceless Quadrupole moment (field-independent basis, Debye-Ang):
   XX=     1.9452   YY=    -3.4778   ZZ=     1.5326
   XY=     4.8215   XZ=     0.0000   YZ=     0.0000
 Octapole moment (field-independent basis, Debye-Ang**2):
  XXX=     0.0000  YYY=     0.0000  ZZZ=     0.0000  XYY=     0.0000
  XXY=     0.0000  XXZ=     0.0000  XZZ=     0.0000  YZZ=     0.0000
  YYZ=     0.0000  XYZ=     0.0000
 Hexadecapole moment (field-independent basis, Debye-Ang**3):
 XXXX=-21294.4305 YYYY=*********** ZZZZ=-19713.7821 XXXY=    50.3524
 XXXZ=     0.0000 YYYX=   180.9205 YYYZ=     0.0000 ZZZX=     0.0000
 ZZZY=     0.0000 XXYY=-26587.1546 XXZZ= -6845.8383 YYZZ=-26329.8384
 XXYZ=     0.0000 YYXZ=     0.0000 ZZXY=     6.8062
 N-N= 3.011792284579D+04 E-N=-7.242684426247D+04  KE= 5.173672811341D+03
 Symmetry AG   KE= 1.371647114340D+03
 Symmetry BG   KE= 1.214487218707D+03
 Symmetry AU   KE= 1.214363252146D+03
 Symmetry BU   KE= 1.373175226148D+03
  Exact polarizability: 836.969  20.8651312.872   0.000   0.000 811.616
 Approx polarizability:2971.352 -45.5752983.449   0.000   0.0002978.129
 Tuple error for IPart= 1 tuple: CalDFT -- LT2D expected length    178929
found length     89465
 Error termination in TplErr.
 Error termination via Lnk1e at Thu Mar  3 19:02:13 2005.

Can someone tell me why this error is occurring and how I might fic it?

Thanks,

Connie




From chemistry-request@ccl.net Thu Mar  3 20:32:59 2005
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Date: Fri, 04 Mar 2005 00:26:23 +0000
From: "Dimitrios Vlachakis" <vlachakisd1 * Cardiff.ac.uk>
To: <CHEMISTRY * ccl.net>
Cc: <Narasinga.Rao * scynexis.com>
Subject: CCL:Re:Sharing files between Linix and Windows partitions
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Dear Narasinga,

> From linux you can edit the fstab file located in:

/etc/fstab

you can use either pico or gedit:
pico /etc/fstab
gedit /etc/fstab

just add the following line on the bottom of the file:

/dev/hda1 /mnt/c vfat defaults 0 0 

and save changes.

then type:

mkdir /mnt/windows

to create a folder called "windows" were to mount the Win partition. finally,
type:

mount /mnt/windows

and you should be able to access all files saved in the linux partition and
launch them using Win software.
Forgot to mention that all of the above works only if the Windows partition is
in FAT16 or FAT32 format. If it is in NTFS format, you must make sure that your
kernel supports it and even if it does you will have read-only access to the
Windows partition.

Now, if you want to access linux files from the Windows partition you can use
one of the numerous freeware applets to help you do it. have a look at:
http://linuxcompatible.org/thread211-1.html


Hope that helps

Dimitrios Vlachakis,
Cardiff University


Dimitrios Vlachakis                
PhD student in Molecular Modelling 
Medicinal Chemistry Group          
Welsh School of Pharmacy           
Cardiff University                 
                                   
Redwood Building                   
King Edward VII Avenue             
CF10 3XF                           
Cardiff                            
Wales, UK                          
                                   
tel. +44 2920 877221               
tel. +44 2920 874551 (lab)         
fax. +44 2920 874537               

...................................................................................
>>> Narasinga Rao <Narasinga.Rao * scynexis.com> 03/03/05 3:01 PM >>>
Dear CCLers,

I would like to find out if it is possible to share files between Windows
and Linux partitions on the same system? For example, is there a way to
launch a browser(say, IE) in the Windows partition and have it run off the
Apachee web server running on the Linux partition of that system?

Thanks for any suggestions.

Narasinga Rao
Scynexis Inc.


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From chemistry-request@ccl.net Fri Mar  4 09:29:17 2005
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 04 Mar 2005 14:20:45 +0200 (MET-DST)
Date: Fri, 04 Mar 2005 14:20:45 +0200 (MET-DST)
From: forli :a: unisi.it
Subject: RE: CCL:addiong ions to simulation box
To: lubos.vrbka :a: uochb.cas.cz, chemistry :a: ccl.net
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In GROMACS there is an utility (genbox) to put randomly in to the
simulation box a precise number of small molecules.
Before to include this structures, you must to generate topologies at
PRODRG server
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html
Probably you must to include forcefield paramenter tools, but I don't
know how easy that could be (I'm going to try...)
I guess you GROMACS if you need to manage long time dynamics with big
systems, because of speed and stability of code.
Hope this help,
Ciao

Stefano



--

***********************************
 Stefano Forli
 Dip. Farmaco Chimico Tecnologico  
 Universita' degli Studi di Siena  
 Via Aldo Moro                    
 I-53100 Siena, Italy              
 Phone: ++39 0577 234307      
 Fax: ++39 0577 234333   
 e-mail: forli :a: unisi.it
***********************************


From chemistry-request@ccl.net Fri Mar  4 17:01:40 2005
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Date: Fri, 4 Mar 2005 12:14:20 -0800 (PST)
From: liaoyi|at|u.washington.edu
To: CHEMISTRY|at|ccl.net
Subject: calculate dipole moment by semiempiral methods
Message-ID: <Pine.LNX.4.43.0503041214200.11226|at|hymn07.u.washington.edu>
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Hi, there:
  Could any body tell me some works that evaluating molecular dipole moment caculation by semiempiral methods especially AM1? I will really appreciate
Best Regards 
Yi






From chemistry-request@ccl.net Fri Mar  4 11:47:46 2005
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From chemistry-request@ccl.net Fri Mar  4 11:53:44 2005
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Subject: RE: Sharing files between Linix and Windows partitions
Date: Fri, 4 Mar 2005 08:53:28 -0800
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Dear Narasinga,

> I would like to find out if it is possible to share files 
> between Windows
> and Linux partitions on the same system? For example, is 
> there a way to
> launch a browser(say, IE) in the Windows partition and have 
> it run off the
> Apachee web server running on the Linux partition of that system?

Linux can mount windows partitions on standard mount points although the
support will depend on your kernel version and/or what is compiled in. NTFS
partitions can be mounted read only, you can also mount them as read write
but this is dangerous.

For Windows you can use a program called Explore2fs
http://uranus.it.swin.edu.au/~jn/linux/explore2fs.htm which allows you to
read Ext2 (and I believe Ext3, since it should be backwards compatible with
Ext2) file systems under windows.

I hope this helps.
All the best
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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