From owner-chemistry@ccl.net Mon Jul 1 08:10:00 2013 From: "Sunny Jeon jeonsunny .. naver.com" To: CCL Subject: CCL: amber cntrl error... Message-Id: <-48881-130701012451-3697-XEGze+UI5r58Ul8PhtoYgA*server.ccl.net> X-Original-From: "Sunny Jeon" Date: Mon, 1 Jul 2013 01:24:50 -0400 Sent to CCL by: "Sunny Jeon" [jeonsunny/a\naver.com] Hello. I am a graduate student in South Korea. A few month ago, I'm beginning Amber10. Previously, input file which someone used in Amber7 is not working in Amber 10. Error message appears...like this.. Here is the input file: 11mer minimization &cntrl imin = 1, maxcyc = 2000, ncyc = 1000, ntb = 1, ntr = 1, cut = 10.0, restraint_wt=1.0, / Hold the DNA fixed 500.0 RES 1 22 END END error in reading namelist cntrl Could you help me to solve this problem.. I just send you this mail even though I don't know whom I can ask this problem... Thank you for reading... From owner-chemistry@ccl.net Mon Jul 1 10:44:00 2013 From: "Kshatresh Dutta Dubey kshatresh^-^gmail.com" To: CCL Subject: CCL: amber cntrl error... Message-Id: <-48882-130701100713-15730-ipVMGbFX4vMpM1EbNDTfWQ-$-server.ccl.net> X-Original-From: Kshatresh Dutta Dubey Content-Type: multipart/alternative; boundary=089e015383923b935304e073bee1 Date: Mon, 1 Jul 2013 19:37:04 +0530 MIME-Version: 1.0 Sent to CCL by: Kshatresh Dutta Dubey [kshatresh:+:gmail.com] --089e015383923b935304e073bee1 Content-Type: text/plain; charset=ISO-8859-1 Hi Sunny.. It seems that you are using input as used in the amber tutorial. You can post questions related to amber on amber_._ambermd.org I recommend to follow this link http://ambermd.org/tutorials/ . It will help you lot. On Mon, Jul 1, 2013 at 10:54 AM, Sunny Jeon jeonsunny .. naver.com < owner-chemistry_._ccl.net> wrote: > > Sent to CCL by: "Sunny Jeon" [jeonsunny/a\naver.com] > Hello. > > I am a graduate student in South Korea. A few month ago, I'm beginning > Amber10. > > Previously, input file which someone used in Amber7 is not working in > Amber 10. > > Error message appears...like this.. > > > > Here is the input file: > > 11mer minimization > &cntrl > imin = 1, > maxcyc = 2000, > ncyc = 1000, > ntb = 1, > ntr = 1, > cut = 10.0, > restraint_wt=1.0, > / > Hold the DNA fixed > 500.0 > RES 1 22 > END > END > > error in reading namelist cntrl > > > Could you help me to solve this problem.. > > I just send you this mail even though I don't know whom I can ask this > problem... > > Thank you for reading...> > > -- With best regards ******************************************************************************************************************* Kshatresh Dutta Dubey, PhD Post Doctoral Fellow Indian Institute of Technology Kanpur Kanpur, India --089e015383923b935304e073bee1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Sunny..

It seems that you are = using input as used in the amber tutorial. You can post questions related t= o amber on=A0amber_._ambermd.org=

I recommend to follow this l= ink=A0http://ambermd.org/t= utorials/=A0. It will help you lot.


On Mon,= Jul 1, 2013 at 10:54 AM, Sunny Jeon jeonsunny .. naver.com <owner-chemistry_._ccl.net> wrote:

Sent to CCL by: "Sunny =A0Jeon" [jeonsunny/a\naver.com]
Hello.

I am a graduate student in South Korea. A few month ago, I'm beginning = Amber10.

Previously, input file which someone used in Amber7 is not working in Amber= 10.

Error message appears...like this..



Here is the input file:

11mer minimization
=A0 &cntrl
=A0 imin =A0 =3D 1,
=A0 maxcyc =3D 2000,
=A0 ncyc =A0 =3D 1000,
=A0 ntb =A0 =A0=3D 1,
=A0 ntr =A0 =A0=3D 1,
=A0 cut =A0 =A0=3D 10.0,
=A0 restraint_wt=3D1.0,
/
Hold the DNA fixed
500.0
RES 1 22
END
END

=A0error in reading namelist cntrl


Could you help me to solve this problem..

I just send you this mail even though I don't know whom I can ask this = problem...

Thank you for reading...



-=3D This is automatically added to each message by the mailing script =3D-=
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--
With best regards
*************************************= ***************************************************************************= ***
Kshatresh Dutta Dubey, PhD
Post Doctoral Fellow
Ind= ian Institute of Technology Kanpur
Kanpur, India


<= /div>
--089e015383923b935304e073bee1-- From owner-chemistry@ccl.net Mon Jul 1 11:18:01 2013 From: "niko prasetyo nikoprasetyo89###gmail.com" To: CCL Subject: CCL: amber cntrl error... Message-Id: <-48883-130701094454-13946-y39BanZ7RKvz3T38LgOKrQ^-^server.ccl.net> X-Original-From: niko prasetyo Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 1 Jul 2013 20:44:47 +0700 MIME-Version: 1.0 Sent to CCL by: niko prasetyo [nikoprasetyo89=-=gmail.com] maybe you should read Amber10 manual first. On 7/1/13, Sunny Jeon jeonsunny .. naver.com wrote: > > Sent to CCL by: "Sunny Jeon" [jeonsunny/a\naver.com] > Hello. > > I am a graduate student in South Korea. A few month ago, I'm beginning > Amber10. > > Previously, input file which someone used in Amber7 is not working in Amber > 10. > > Error message appears...like this.. > > > > Here is the input file: > > 11mer minimization > > &cntrl > > imin = 1, > > maxcyc = 2000, > > ncyc = 1000, > > ntb = 1, > > ntr = 1, > > cut = 10.0, > > restraint_wt=1.0, > > / > > Hold the DNA fixed > > 500.0 > > RES 1 22 > > END > > END > > > error in reading namelist cntrl > > > Could you help me to solve this problem.. > > I just send you this mail even though I don't know whom I can ask this > problem... > > Thank you for reading...> > > From owner-chemistry@ccl.net Mon Jul 1 12:37:01 2013 From: "Herbert Fruchtl herbert.fruchtl===st-andrews.ac.uk" To: CCL Subject: CCL: amber cntrl error... Message-Id: <-48884-130701123512-6625-c4QkJcc6cBvL6QEQ0sYkBA|server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 01 Jul 2013 17:34:46 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl|,|st-andrews.ac.uk] This is a list for asking questions. If you think a question does not deserve a reply, don't reply. Herbert On 01/07/13 14:44, niko prasetyo nikoprasetyo89###gmail.com wrote: > > Sent to CCL by: niko prasetyo [nikoprasetyo89=-=gmail.com] > maybe you should read Amber10 manual first. > > On 7/1/13, Sunny Jeon jeonsunny .. naver.com wrote: >> >> Sent to CCL by: "Sunny Jeon" [jeonsunny/a\naver.com] >> Hello. >> >> I am a graduate student in South Korea. A few month ago, I'm beginning >> Amber10. >> >> Previously, input file which someone used in Amber7 is not working in Amber >> 10. >> >> Error message appears...like this.. >> >> >> >> Here is the input file: >> >> 11mer minimization >> >> &cntrl >> >> imin = 1, >> >> maxcyc = 2000, >> >> ncyc = 1000, >> >> ntb = 1, >> >> ntr = 1, >> >> cut = 10.0, >> >> restraint_wt=1.0, >> >> / >> >> Hold the DNA fixed >> >> 500.0 >> >> RES 1 22 >> >> END >> >> END >> >> >> error in reading namelist cntrl >> >> >> Could you help me to solve this problem.. >> >> I just send you this mail even though I don't know whom I can ask this >> problem... >> >> Thank you for reading...> > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Mon Jul 1 13:26:00 2013 From: "Jan Jensen Jhjensen^-^chem.ku.dk" To: CCL Subject: CCL: Computational Chemistry Highlights: June issue Message-Id: <-48885-130701124400-10314-dYDYds+nAx6kkkCB2236Bw(0)server.ccl.net> X-Original-From: "Jan Jensen" Date: Mon, 1 Jul 2013 12:43:57 -0400 Sent to CCL by: "Jan Jensen" [Jhjensen\a/chem.ku.dk] The June issue of Computational Chemistry Highlights is out. http://www.compchemhighlights.org/2013_06_01_archive.html CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here. Table of content for this issue features contributions from CCH editors Steven Bachrach, Jonathan Goodman, and Jan Jensen: Molecularspace.org http://www.compchemhighlights.org/2013/06/molecularspaceorg.html Three interesting recent Angew. Chem. papers http://www.compchemhighlights.org/2013/06/three-interesting-recent-angew-chem.html Unraveling the Enigmatic Mechanism of LAsparaginase II with QM/QM calculations http://www.compchemhighlights.org/2013/06/the-enigmatic-mechanism-of.html Interested in more? There are many ways to subscribe to CCH updates. http://www.compchemhighlights.org/p/get-cch-updates.html From owner-chemistry@ccl.net Mon Jul 1 14:11:00 2013 From: "Paolo Tosco paolo.tosco!^!unito.it" To: CCL Subject: CCL: MMFF94 charge assignment doubts Message-Id: <-48886-130701140355-15309-hScSqkiBlLHfV91k1KEFzQ!=!server.ccl.net> X-Original-From: Paolo Tosco Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 01 Jul 2013 20:03:47 +0200 MIME-Version: 1.0 Sent to CCL by: Paolo Tosco [paolo.tosco_+_unito.it] Dear all, I have a molecule which is giving me some trouble in correctly assigning MMFF94 charges. The molecule is protonated biguanide, which has been experimentally isolated and crystallized (see http://dx.doi.org/10.1039/DT9780000989): protbiguanide 3D protbiguanide 16 15 0 0 0 0 0 0 0 0999 V2000 2.0381 -1.1825 -0.5455 N 0 0 0 0 0 0 0 0 0 0 0 0 1.8449 -2.0865 -0.9585 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2824 -0.6072 -0.2018 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3256 -0.7497 -0.4576 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6392 0.5653 -0.3022 N 0 0 0 0 0 0 0 0 0 0 0 0 4.8658 0.9592 0.1243 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6866 0.1735 0.8651 N 0 0 0 0 0 0 0 0 0 0 0 0 5.3940 -0.6956 1.3014 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6048 0.5074 1.1522 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2787 2.2179 -0.1625 N 0 3 0 0 0 0 0 0 0 0 0 0 6.1779 2.5691 0.1567 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7395 2.8648 -0.7292 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0119 1.2719 -0.6673 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3000 -1.6959 -0.6275 N 0 3 0 0 0 0 0 0 0 0 0 0 5.2717 -1.4654 -0.8245 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0826 -2.6877 -0.7101 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 4 1 0 0 0 0 1 3 1 0 0 0 0 4 5 1 0 0 0 0 4 14 2 0 0 0 0 5 13 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 6 10 2 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 14 15 1 0 0 0 0 14 16 1 0 0 0 0 M CHG 1 10 1 M CHG 1 14 1 M END $$$$ According to the MMFF papers by Halgren, all NGD+ atoms should be assigned a formal charge of 0.333; this is actually what both Schrödinger Maestro and MolSoft ICM do. However, doing so gives a non-integer total formal charge of 1.667, and the partial charge distribution is the following: -0.87, 0.45, 0.20, 0.15, 0.20, 0.15, -0.87, 0.45, 1.07, -0.79, 0.45, 1.20, -0.97, 0.45, 0.45, -0.97, 0.45, 0.45 as resulting by the application of equation 15 on page 622 of the MMFF.V paper by Halgren. Indeed, also these partial charges sum to 1.67. If I run the same calculation in MOE, formal charges are instead assigned a value of 0.4 (that is, 2.0/5), and the resulting partial charge distribution is: -0.9, 0.45, 0.45, 1.2, -0.85, 1.2, -0.9, 0.45, 0.45, -0.9, 0.45, 0.45, 0.45, -0.9, 0.45, 0.45 which sums up to 2.0 and has indeed been correctly computed by means of equation 15; just the starting formal charges were 0.4 instead of 0.333. While the second charge distribution is formally more correct, since total formal charge must be integer, it does not strictly follow MMFF94 rules. Looking at the official MMFF94 validation suite, there is no such case - when guanidine groups appear, they are always "complete" guanidines (that is, three NGD+ atoms for each guaninidine group), hence the problem does not appear. Clearly, the issue shows up when the number of NGD+ atoms is not a multiple of 3. Probably, to get meaningful and reproducible charge distributions one should always use NGD+ atom types (and similar cases, as inthe NGD+,N5+,N5+ triplet of 2-aminoimidazolium) in multiples of 3, to avoid either incurring in the issue of fractional total formal charge, or scaling formal charges, a procedure which is not mentioned in the MMFF papers. Any insight on this matter is highly appreciated. Best regards, Paolo -- ========================================================== Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670 7687 | E-mail:paolo.tosco^-^unito.it http://open3dqsar.org |http://open3dalign.org ==========================================================