From owner-chemistry@ccl.net Tue Jan 21 11:09:00 2014 From: "Muhammad Jawad jawadfs- -cemb.edu.pk" To: CCL Subject: CCL: AMDET Predictor Software Request Message-Id: <-49580-140121043135-25860-fzTxyaCvmhbO8RD7tOGhGA^_^server.ccl.net> X-Original-From: Muhammad Jawad Content-Type: multipart/alternative; boundary=001a11c1628e228b3604f077acc9 Date: Tue, 21 Jan 2014 14:31:26 +0500 MIME-Version: 1.0 Sent to CCL by: Muhammad Jawad [jawadfs_-_cemb.edu.pk] --001a11c1628e228b3604f077acc9 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear Wolf Ihlenfeldt, I am new in the field of Bioinformatics, and recently working on QSAR. I read about ADMET predictor free trial but couldn't find its downloading option. Well your post is pretty much distressing for me however I must clarify that I just wanted to know about trial versions not the cracked one. I also wrote an email to the company and didn't get response thats why I wrote on CCL. I hope things should be clarify now. Regards Jawad On Mon, Jan 20, 2014 at 2:56 PM, Wolf Ihlenfeldt wdi]![xemistry.com < owner-chemistry~!~ccl.net> wrote: > > Sent to CCL by: Wolf Ihlenfeldt [wdi\a/xemistry.com] > Why did this request get though the filters? I read this post as a > blunt request for a cracked copy of an expensive commercial product. > > If you need such software for your research and cannot afford normal > commercial pricing, the only acceptable way is to contact the vendor > directly and talk to them. Most have special conditions for academia, > and may even provide you, on a case-by-case basis, a free copy. > > However, after such a post, this is in all probability no longer be an > option for you, since you will be seen as an uncontrollable risk to > illegally disseminate software you received under special conditions > and are now blacklisted throughout the industry. > > You have just officially shot yourself in your own foot. > > > > On Mon, Jan 20, 2014 at 9:37 AM, Muhammad Jawad jawadfs=3D=3D=3Dcemb.edu.= pk > wrote: > > > > Sent to CCL by: "Muhammad Jawad" [jawadfs-$-cemb.edu.pk] > > Hi, > > > > Can anybody send me ADMET Predictor software. I have to use it for > study. I will be very thankful. > > > http://www.simulations-plus.com/Products.aspx?ADMET%20Predictor&grpID=3D1= &cID=3D11&pID=3D13 > > > > Regards > > Muhammad Jawad> > > > > > > -- > Wolf-D. Ihlenfeldt - Xemistry GmbH - wdi|a|xemistry.com > Phone: +49 6174 201455 - Fax +49 6174 209665 > --- > xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. Ihlenf= eldt > Address: Hainholzweg 11, D-61462 K=F6nigstein, Germany > HR K=F6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 *Muhammad Jawad* *+92 314 312 1690* *M. Phil Research Scholar* *Session (2012-2014)* *Molecular Biology (Bioinformatics) * *National Centre of Excellence in Molecular Biology (CEMB)**University of the Punjab (PU), Lahore* *www.cemb.edu.pk * *Pakistan* --001a11c1628e228b3604f077acc9 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable
Dear=A0Wolf Ihlenfeldt,

<= /font>
I am= new in the field of Bioinformatics, and recently working on QSAR. I read a= bout ADMET predictor free trial but couldn't find its downloading optio= n. Well your post is pretty much distressing for me=A0however I must clarify that I= just wanted to know about trial versions not=A0the cracked one. I also wro= te an email to the company and didn't get response thats why I wrote on= CCL. I hope things should be clarify now.=A0
Regards
Jawad

On Mon, Jan 20, 2014 at 2:56 PM, Wolf Ihle= nfeldt wdi]![xemistry.com <owner= -chemistry~!~ccl.net> wrote:

Sent to CCL by: Wolf Ihlenfeldt [wdi\a/xemistry.com]
Why did this request get though the filters? I read this post as a
blunt request for a cracked copy of an expensive commercial product.

If you need such software for your research and cannot afford normal
commercial pricing, the only acceptable way is to contact the vendor
directly and talk to them. Most have special conditions for academia,
and may even provide you, on a case-by-case basis, =A0a free copy.

However, after such a post, this is in all probability no longer be an
option for you, since you will be seen as an uncontrollable risk to
illegally disseminate software you received under special conditions
and are now blacklisted throughout the industry.

You have just officially shot yourself in your own foot.



On Mon, Jan 20, 2014 at 9:37 AM, Muhammad Jawad jawadfs=3D=3D=3Dcemb.edu.pk
<owner-chemistry|a|ccl.net<= /a>> wrote:
>
> Sent to CCL by: "Muhammad =A0Jawad" [jawadfs-$-cemb.edu.pk]
> Hi,
>
> Can anybody send me ADMET Predictor software. I have to use it for stu= dy. I will be very thankful.
> http://www.= simulations-plus.com/Products.aspx?ADMET%20Predictor&grpID=3D1&cID= =3D11&pID=3D13
>
> Regards
> Muhammad Jawad>
>



--
Wolf-D. Ihlenfeldt - =A0Xemistry GmbH - wdi|a|xemistry.com
Phone: +49 61= 74 201455 - Fax +49 6174 209665
---
xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. Ihlenfel= dt
Address: Hainholzweg 11, D-61462 K=F6nigstein, Germany
HR K=F6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719



-=3D This is automatically added to each message by the mailing script =3D-=
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=A0 =A0 =A0 h= ttp://www.ccl.net/spammers.txt

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--
=
Muhammad Jawad
+92 314 312 1690=
M. Phil Research Scholar
Session (2012-2014)
Molecular Biology (Bioinformat= ics)=A0
National Centre of Excellence in Molecular Biology = (CEMB)
= University of=A0= the Punjab (PU), Lahore
Pakistan
--001a11c1628e228b3604f077acc9-- From owner-chemistry@ccl.net Tue Jan 21 11:44:00 2014 From: "Simon Cross simon!=!moldiscovery.com" To: CCL Subject: CCL: MoKa 2.5 for pKa, tautomer, logP, logD and IEP modelling Message-Id: <-49581-140121061428-13573-usxS4qVCIS3f7UlSwkzbZQ+/-server.ccl.net> X-Original-From: Simon Cross Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 21 Jan 2014 12:14:14 +0100 MIME-Version: 1.0 Sent to CCL by: Simon Cross [simon---moldiscovery.com] Hi Everyone, just to let you know that we have released MoKa 2.5 for pKa, tautomer, logP, logD and IEP modelling. As with every version, many literature compounds have been experimentally retested to improve our confidence in the models; with this release 40 of the 55 models have been recomputed based on this new data. Additionally, structural input has been improved to make it more efficient and less affected by external factors; for example, counterions are now automatically stripped during LogP-LogD and IEP calculations. Recognized ionizable centres that are predicted with lower certainty are now shown, to enable users to see where they should focus their efforts to improve the provided models. The molecule isoelectric point (IEP) is now computed. Finally, the model training module Kibitzer is now accessible command-line, enabling users to automate custom model building as new company data is obtained. More information about MoKa can be found here: http://www.moldiscovery.com/soft_moka.php Kind regards, Simon Dr. Simon Cross Snr Scientist & Product Manager Molecular Discovery Ltd Email: simon[at]moldiscovery[dot]com Molecular Discovery provides robust, high-quality and innovative computational methods addressing pharmaceutical needs in the field of drug discovery, including methods for virtual screening, lead optimisation, ADME modelling and metabolism research. Molecular Discovery software products offer calculation of accurate Molecular Interaction Fields for structure-based design (GRID), ligand-based and structure-based virtual screening (FLAP), pharmacophore elucidation (FLAP), metabolism prediction (MetaSite), metabolite identification (Mass-MetaSite), scaffold hopping (SHOP), pKa prediction (MoKa), 3D-QSAR modeling (FLAP, Pentacle) to improve efficiency in modern drug discovery. More information can be found on the main page: http://www.moldiscovery.com From owner-chemistry@ccl.net Tue Jan 21 13:43:01 2014 From: "Billy McCann thebillywayne**gmail.com" To: CCL Subject: CCL: AMDET Predictor Software Request Message-Id: <-49582-140121133703-18403-kG5VhhWi3X2YezC8xLlChw|,|server.ccl.net> X-Original-From: Billy McCann Content-Type: multipart/alternative; boundary=001a11c330060863b304f07f4bac Date: Tue, 21 Jan 2014 13:36:42 -0500 MIME-Version: 1.0 Sent to CCL by: Billy McCann [thebillywayne ~~ gmail.com] --001a11c330060863b304f07f4bac Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Muhammed, http://www.simulations-plus.com/softwareform.aspx Billy Wayne McCann, Ph.D. Google+ PGP Key irc://irc.freenode.net:bwayne "A rich man will always desire what his wealth cannot acquire." ~ Faust (Goethe) [00(01|10)11] On Tue, Jan 21, 2014 at 4:31 AM, Muhammad Jawad jawadfs- -cemb.edu.pk < owner-chemistry . ccl.net> wrote: > Dear Wolf Ihlenfeldt, > > I am new in the field of Bioinformatics, and recently working on QSAR. I > read about ADMET predictor free trial but couldn't find its downloading > option. Well your post is pretty much distressing for me however I must > clarify that I just wanted to know about trial versions not the cracked > one. I also wrote an email to the company and didn't get response thats w= hy > I wrote on CCL. I hope things should be clarify now. > Regards > Jawad > > > On Mon, Jan 20, 2014 at 2:56 PM, Wolf Ihlenfeldt wdi]![xemistry.com < > owner-chemistry^ccl.net> wrote: > >> >> Sent to CCL by: Wolf Ihlenfeldt [wdi\a/xemistry.com] >> Why did this request get though the filters? I read this post as a >> blunt request for a cracked copy of an expensive commercial product. >> >> If you need such software for your research and cannot afford normal >> commercial pricing, the only acceptable way is to contact the vendor >> directly and talk to them. Most have special conditions for academia, >> and may even provide you, on a case-by-case basis, a free copy. >> >> However, after such a post, this is in all probability no longer be an >> option for you, since you will be seen as an uncontrollable risk to >> illegally disseminate software you received under special conditions >> and are now blacklisted throughout the industry. >> >> You have just officially shot yourself in your own foot. >> >> >> >> On Mon, Jan 20, 2014 at 9:37 AM, Muhammad Jawad jawadfs=3D=3D=3Dcemb.edu= .pk >> wrote: >> > >> > Sent to CCL by: "Muhammad Jawad" [jawadfs-$-cemb.edu.pk] >> > Hi, >> > >> > Can anybody send me ADMET Predictor software. I have to use it for >> study. I will be very thankful. >> > >> http://www.simulations-plus.com/Products.aspx?ADMET%20Predictor&grpID=3D= 1&cID=3D11&pID=3D13 >> > >> > Regards >> > Muhammad Jawad> >> > >> >> >> >> -- >> Wolf-D. Ihlenfeldt - Xemistry GmbH - wdi|a|xemistry.com >> Phone: +49 6174 201455 - Fax +49 6174 209665 >> --- >> xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr.= W. D. Ihlenfeldt >> Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany >> HR K=C3=B6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D- >> E-mail to subscribers: CHEMISTRY^ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST^ccl.net or use>> >> >> > > > -- > > *Muhammad Jawad * > *+92 314 312 1690 <%2B92%20314%20312%201690> * > *M. Phil Research Scholar * > > *Session (2012-2014) * > > *Molecular Biology (Bioinformatics) * > *National Centre of Excellence in Molecular Biology (CEMB) **University > of the Punjab (PU), Lahore* > *www.cemb.edu.pk * > *Pakistan* > --001a11c330060863b304f07f4bac Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Muhammed,

http://www.simulations-plus.com/softwareform.aspx
<= /div>


Billy Wayne McCann, Ph.D.
= Goo= gle+
PG= P Key
irc://irc.= freenode.net:bwayne

"A rich man will always desire what his wealth cannot acqui= re." ~ Faust (Goethe)

[= 00(01|10)11]


On Tue, Jan 21, 2014 at 4:31 AM, Muhamma= d Jawad jawadfs- -cemb.edu.pk <o= wner-chemistry . ccl.net> wrote:
Dear=C2=A0Wolf Ihlenfeldt,

I a= m new in the field of Bioinformatics, and recently working on QSAR. I read = about ADMET predictor free trial but couldn't find its downloading opti= on. Well your post is pretty much distressing for me=C2=A0however I must clarify th= at I just wanted to know about trial versions not=C2=A0the cracked one. I a= lso wrote an email to the company and didn't get response thats why I w= rote on CCL. I hope things should be clarify now.=C2=A0
Regards
Jawad

On Mon, Jan 20, 2014 at 2:56 PM, Wolf Ihle= nfeldt wdi]![xemistry.com= <owner-chemistry^ccl.net> wrote:

Sent to CCL by: Wolf Ihlenfeldt [wdi\a/xemistry.com]
Why did this request get though the filters? I read this post as a
blunt request for a cracked copy of an expensive commercial product.

If you need such software for your research and cannot afford normal
commercial pricing, the only acceptable way is to contact the vendor
directly and talk to them. Most have special conditions for academia,
and may even provide you, on a case-by-case basis, =C2=A0a free copy.

However, after such a post, this is in all probability no longer be an
option for you, since you will be seen as an uncontrollable risk to
illegally disseminate software you received under special conditions
and are now blacklisted throughout the industry.

You have just officially shot yourself in your own foot.



On Mon, Jan 20, 2014 at 9:37 AM, Muhammad Jawad jawadfs=3D=3D=3Dcemb.edu.pk
<owner-chemistry|a|ccl.net<= /a>> wrote:
>
> Sent to CCL by: "Muhammad =C2=A0Jawad" [jawadfs-$-cemb.edu.pk]
> Hi,
>
> Can anybody send me ADMET Predictor software. I have to use it for stu= dy. I will be very thankful.
> http://www.= simulations-plus.com/Products.aspx?ADMET%20Predictor&grpID=3D1&cID= =3D11&pID=3D13
>
> Regards
> Muhammad Jawad>
>



--
Wolf-D. Ihlenfeldt - =C2=A0Xemistry GmbH - wdi|a|xemistry.com
Phone: +49 6174 201455 - Fax +49 6174 209665
---
xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr. W.= D. Ihlenfeldt
Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany
HR K=C3=B6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY^ccl.net or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

E-mail to administrators: CHEMISTRY-REQUEST^ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/





--
Muhammad Jawad
+92 314 = 312 1690
M. Phil Research Scholar
Session (2012-2014)
Molecular Biology (Bioinformat= ics)=C2=A0
National Centre of Excellence in Molecular Biology = (CEMB)
= University of=C2=A0<= /b>the Punjab (PU), Lahore
Pakistan

--001a11c330060863b304f07f4bac-- From owner-chemistry@ccl.net Tue Jan 21 19:19:00 2014 From: "Lluis Raich lraich++hotmail.es" To: CCL Subject: CCL: irc false minimum even tightening and changing maxstep size params Message-Id: <-49583-140121103934-30813-hiLbiPL/uBfX6snktFTInw(_)server.ccl.net> X-Original-From: "Lluis Raich" Date: Tue, 21 Jan 2014 10:39:33 -0500 Sent to CCL by: "Lluis Raich" [lraich/a\hotmail.es] Good evening, I am trying to find a reaction path to make Umbrella Sampling on it, but when found the TS, IRC fails and stops at the second step (as other people has posted before) because of the flat PES (in part because of the implicit solvent, water). The point is that this TS is the correct, not just the vibrational modes seems correct but also, making an optimization of TS structures moved a factor of 0.1 of the imaginari eigenvector (forward and reverse), structures falls to expected reactants and products. Trying solutions like thigthening the criterion of a minimum (IOp(1/7)=10), fixing the maxstepsize (I have tryied values from 3 to 100, in principle higher values should be better because the surface at this point is flat) and calculating the Hessian at each point (CalcAll) does not work. As I just want points along the path, the optimization I have performed should be enought (the one I commented before: "moved a factor of 0.1 of the imaginari eigenvector..."), but points are so dispersed and not regular. Even fixing maxstepsize=3, I have seen that the program starts with this value but then it takes whatever he wants (it increases it from 3 to 15 and even more). Is there any manner to fix the step taken in a minimization (no more than 0.05 Angstroms for example) for all the minimization or other advises for the IRC calculation? Thanks in advance, Louis Pd: IRC input and output example: In:#p PBEPBE/6-311+G** IRC(calcall,maxpoints=50,forward,hpc,stepsize=3) iop(1/7=10) scrf=(solvent=water) Out: Energy RxCoord 1 0.00000 0.00000 2 0.00000 0.05263