Yea only NVT because you can't (or at least I couldn't) figure out the virial contributions that generate out of an external electric field.
Charlie
________________________________________
From: Neville Bethel [nevillebethel.gmail.com]
Sent: Wednesday, May 10, 2017 6:54 PM
To: amber.ambermd.org
Subject: Re: [AMBER] External electric fields on CUDA enabled PMEMD
Hi Charlie,
Thanks for letting me know about these update.
I tried running with this latest updates, but I got the following error:
ERROR: External electric fields cannot be used when npt > 0
Are the electric fields only supported in NVT?
Cheers,
Neville
>
> Date: Mon, 1 May 2017 02:32:00 +0000
> From: Charles Lin <clin92.ucsd.edu>
> Subject: Re: [AMBER] External electric fields on CUDA enabled PMEMD
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <235587F1F2398A4E9810CC1297B4DB827928ECAE.xmail-mbx-bv1.AD.
> UCSD.EDU>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi, external electric fields support were added in Amber 16 as of update.1
> and update.2 (June 2016)
>
> -Charlie
> ________________________________________
> From: Neville Bethel [nevillebethel.gmail.com]
> Sent: Sunday, April 30, 2017 1:14 PM
> To: amber.ambermd.org
> Subject: [AMBER] External electric fields on CUDA enabled PMEMD
>
> Dear amber developers,
>
> I am interested in using external electric fields in CUDA enabled PMEMD for
> membrane simulations.
>
> I noticed this post from a year ago that mentioned that electric fields
> exist in the CPU version, and that it may be added to GPU enabled PMEMD in
> the near future:
> http://archive.ambermd.org/201605/0005.html
>
> Has any progress been made on this? Could I expect to see this in a patch
> for Amber 16, or would it be in the next version of Amber?
>
> Thank you,
> Neville
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 1 May 2017 02:28:02 -0400
> From: Alexander Adams <xadams.umich.edu>
> Subject: [AMBER] Missing File: charmmlipid2amber.csv
> To: amber.ambermd.org
> Message-ID:
> <CAKH_DmeYh90aXvjtgY5EV4ooRLPcDBJK7AVGjVAVoRTmJuOtmw.mail.gmail.
> com>
> Content-Type: text/plain; charset=UTF-8
>
> Hello all,
>
> I am trying to convert a Charmm-Gui membrane system to amber notation for
> use in the H++ web tool. I have downloaded AmberTools 17 which contains the
> charmmlipid2amber.py script, but if references a csv replacement file that
> does not appear to be in the download. I have searched where the script
> points and cannot find it.
>
> If someone could direct me to the file within the download or where it is
> otherwise available I would appreciate it. Thanks in advance.
>
> Alex Adams
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 1 May 2017 07:03:57 +0000
> From: "Elvis Martis" <elvis.martis.bcp.edu.in>
> Subject: Re: [AMBER] Missing File: charmmlipid2amber.csv
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <MAXPR01MB0218F3739C68F00D6636B70BA3140.MAXPR01MB0218.
> INDPRD01.PROD.OUTLOOK.COM>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi
> Just look in this directory $AMBERHOME/dat/charmmlipid2amber/
> You should find it here.
>
> ? ? Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> ?at?Bombay College of Pharmacy
>
>
> A??Kalina, Santacruz [E], Mumbai 400098, INDIA
> W?www.elvismartis.in
> Skype.?adrian_elvis12
>
>
>
>
> -----Original Message-----
> From: Alexander Adams [mailto:xadams.umich.edu]
> Sent: Monday, May 01, 2017 11:58 AM
> To: amber.ambermd.org
> Subject: [AMBER] Missing File: charmmlipid2amber.csv
>
> Hello all,
>
> I am trying to convert a Charmm-Gui membrane system to amber notation for
> use in the H++ web tool. I have downloaded AmberTools 17 which contains the
> charmmlipid2amber.py script, but if references a csv replacement file that
> does not appear to be in the download. I have searched where the script
> points and cannot find it.
>
> If someone could direct me to the file within the download or where it is
> otherwise available I would appreciate it. Thanks in advance.
>
> Alex Adams
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 1 May 2017 08:11:42 +0100
> From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
> Subject: Re: [AMBER] Restraint in Steered MD/Jarzynski method
> To: <amber.ambermd.org>
> Message-ID: <20170501081142.57b8dde8.Hannes.Loeffler.stfc.ac.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> On Sun, 30 Apr 2017 18:41:18 +0000
> Ramin Salimi <ramin.salimi01.utrgv.edu> wrote:
>
> > Hi Hannes
> >
> > Thanks so very much for the reply because I really need clarification.
> >
> > Regarding the first question, I am confused between either one of
> > these two:
> >
> > 1- minimize, heat up, equilibration. Then pick 'n' frames from the
> > equilibration trajectory, and do SMD on each
>
> The Jarzynski method requires you to start from equilibrated initial
> states. So if you run N non-equilibrium simulations you will need N
> such states. These states should be unbiased (so not restraints),
> independent from each other and representative for the state you start
> from.
>
>
> Cheers,
> Hannes.
>
>
>
> ------------------------------
>
> Message: 7
> Date: Mon, 1 May 2017 22:28:07 +0800 (GMT+08:00)
> From: ??? <zhangzhzh16.lzu.edu.cn>
> Subject: Re: [AMBER] [SPAM] Re: consult about LEaP in amber
> To: "AMBER Mailing List" <amber.ambermd.org>
> Message-ID:
> <469e1952.c582.15bc469504e.Coremail.zhangzhzh16.lzu.edu.cn>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
> These are all files I used in my calculate. And my original purpose is to
> get atom-atom interactions in RNA.
>
> Best Regards
>
>
>
>
> zhangzhuangzhuang
> (lanzhou university)
>
>
> > -----????-----
> > ???: "Elvis Martis" <elvis.martis.bcp.edu.in>
> > ????: 2017-04-26 18:39:01 (???)
> > ???: "AMBER Mailing List" <amber.ambermd.org>
> > ??:
> > ??: [SPAM] Re: [AMBER] consult about LEaP in amber
> >
> > Hi,
> > It's not clear what you want to do. Leap is a module to prepare system
> for various simulations using AMBER and not a tool to compute atom-atom
> interactions.
> > Please send the leap.log file in order to understand what you are trying
> to do.
> >
> >     Best Regards
> >
> >
> >
> > Elvis Martis
> > Ph.D. Student (Computational Chemistry)
> >  at Bombay College of Pharmacy
> >
> >
> > A  Kalina, Santacruz [E], Mumbai 400098, INDIA
> > W www.elvismartis.in
> > Skype. adrian_elvis12
> >
> >
> >
> >
> > -----Original Message-----
> > From: ??? [mailto:zhangzhzh16.lzu.edu.cn]
> > Sent: Wednesday, April 26, 2017 9:20 AM
> > To: amber.ambermd.org
> > Subject: [AMBER] consult about LEaP in amber
> >
> > Hello,
> > I use LEaP to calculate atom-atom interactions energy in RNA.The
> platform is: Amber14 + AmberTool16. the pdb file and tleap.in and result
> file are attached.
> > however.some atom-atom interactions are missed.like atom 197 with atom
> 240 in the 1.eout. I want to konw is this a normal or I did some wrong in
> some parameters?
> > please help and thank you a lot!
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: RNA_amber.rar
> Type: application/octet-stream
> Size: 597509 bytes
> Desc: not available
> Url : http://lists.ambermd.org/mailman/private/amber/
> attachments/20170501/6477e6ad/attachment-0001.obj
>
> ------------------------------
>
> Message: 8
> Date: Mon, 1 May 2017 14:49:51 +0000
> From: "Thakur, Abhishek" <axt651.miami.edu>
> Subject: [AMBER] does not have a type
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID:
> <BN6PR07MB2803A075A3A66EB5D8A6BA8C9E140.BN6PR07MB2803.
> namprd07.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi
> I am trying to make my complex prmtop and inpcrd file.
>
> For that I have done RESP charge calculation for my ligand and then have
> created frcmod and lib file for my ligand.
>
> By while generating complex parameter files it is giving me following
> error.
> I am unable to get it why such problem is coming.
> As I am providing it prmtop and lib file of my ligand.
>
> I am attaching the prmtop, lib and pdb file of my ligand so that if any
> one can find my mistake.
>
>
>
> > saveamberparm R_config C8.prmtop C8.inpcrd
> Checking Unit.
> FATAL: Atom .R<UNK 545>.A<C2 1> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H12 2> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H22 3> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C17 4> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H1 5> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H2 6> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C18 7> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C19 8> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C20 9> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C21 10> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C22 11> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C23 12> does not have a type.
> FATAL: Atom .R<UNK 545>.A<N23 13> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C24 14> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H 15> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C26 16> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C28 17> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C27 18> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C29 19> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C25 20> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C30 21> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C31 22> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C33 23> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C32 24> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C35 25> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C36 26> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C34 27> does not have a type.
> FATAL: Atom .R<UNK 545>.A<N36 28> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C37 29> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H3 30> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C 31> does not have a type.
> FATAL: Atom .R<UNK 545>.A<N2 32> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C3 33> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C5 34> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C7 35> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C6 36> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C8 37> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C4 38> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C9 39> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C10 40> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C11 41> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C12 42> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C15 43> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C14 44> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C13 45> does not have a type.
> FATAL: Atom .R<UNK 545>.A<N14 46> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C1 47> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C16 48> does not have a type.
>
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: UNK_H_renum.pdb
> Type: chemical/x-pdb
> Size: 7371 bytes
> Desc: UNK_H_renum.pdb
> Url : http://lists.ambermd.org/mailman/private/amber/
> attachments/20170501/08e8977d/attachment-0001.pdb
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: UNK.frcmod
> Type: application/octet-stream
> Size: 1058 bytes
> Desc: UNK.frcmod
> Url : http://lists.ambermd.org/mailman/private/amber/
> attachments/20170501/08e8977d/attachment-0002.obj
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: UNK.lib
> Type: application/octet-stream
> Size: 12448 bytes
> Desc: UNK.lib
> Url : http://lists.ambermd.org/mailman/private/amber/
> attachments/20170501/08e8977d/attachment-0003.obj
>
> ------------------------------
>
> Message: 9
> Date: Mon, 1 May 2017 14:56:14 +0000
> From: Sowmya Indrakumar <soemya.kemi.dtu.dk>
> Subject: Re: [AMBER] does not have a type
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <9064D625684B0B4487521D3C950F87D708A44606.ait-pex01mbx03.
> win.dtu.dk>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Abhishek,
> Are you loading this: source leaprc.gaff ??
>
> Regards
> Sowmya
> ________________________________________
> From: Thakur, Abhishek [axt651.miami.edu]
> Sent: Monday, May 01, 2017 4:49 PM
> To: amber.ambermd.org
> Subject: [AMBER] does not have a type
>
> Hi
> I am trying to make my complex prmtop and inpcrd file.
>
> For that I have done RESP charge calculation for my ligand and then have
> created frcmod and lib file for my ligand.
>
> By while generating complex parameter files it is giving me following
> error.
> I am unable to get it why such problem is coming.
> As I am providing it prmtop and lib file of my ligand.
>
> I am attaching the prmtop, lib and pdb file of my ligand so that if any
> one can find my mistake.
>
>
>
> > saveamberparm R_config C8.prmtop C8.inpcrd
> Checking Unit.
> FATAL: Atom .R<UNK 545>.A<C2 1> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H12 2> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H22 3> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C17 4> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H1 5> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H2 6> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C18 7> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C19 8> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C20 9> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C21 10> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C22 11> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C23 12> does not have a type.
> FATAL: Atom .R<UNK 545>.A<N23 13> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C24 14> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H 15> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C26 16> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C28 17> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C27 18> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C29 19> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C25 20> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C30 21> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C31 22> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C33 23> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C32 24> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C35 25> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C36 26> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C34 27> does not have a type.
> FATAL: Atom .R<UNK 545>.A<N36 28> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C37 29> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H3 30> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C 31> does not have a type.
> FATAL: Atom .R<UNK 545>.A<N2 32> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C3 33> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C5 34> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C7 35> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C6 36> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C8 37> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C4 38> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C9 39> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C10 40> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C11 41> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C12 42> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C15 43> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C14 44> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C13 45> does not have a type.
> FATAL: Atom .R<UNK 545>.A<N14 46> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C1 47> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C16 48> does not have a type.
>
>
>
>
> ------------------------------
>
> Message: 10
> Date: Mon, 1 May 2017 14:58:44 +0000
> From: "Thakur, Abhishek" <axt651.miami.edu>
> Subject: Re: [AMBER] does not have a type
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <BN6PR07MB280326F91A98446BC4D738E39E140.BN6PR07MB2803.
> namprd07.prod.outlook.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Sowmya,
>
>
> Yes I am doing that
>
>
> tleap -s -f leaprc.ff14SB.ORIG
> source leaprc.gaff
> loadamberparams UNK.frcmod
> loadoff UNK.lib
> R_config = loadpdb C8_H.pdb
> solvateBox R_config TIP3PBOX 10
> charge R_config
> addIons R_config Cl- 2
> loadAmberParams frcmod.ionsjc_tip3p
> saveamberparm R_config C8.prmtop C8.inpcrd
> savepdb R_config complex.pdb
> quit
>
>
> This is what I am doing.
>
> ________________________________
> From: Sowmya Indrakumar <soemya.kemi.dtu.dk>
> Sent: Monday, May 1, 2017 3:56:14 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] does not have a type
>
> Hi Abhishek,
> Are you loading this: source leaprc.gaff ??
>
> Regards
> Sowmya
> ________________________________________
> From: Thakur, Abhishek [axt651.miami.edu]
> Sent: Monday, May 01, 2017 4:49 PM
> To: amber.ambermd.org
> Subject: [AMBER] does not have a type
>
> Hi
> I am trying to make my complex prmtop and inpcrd file.
>
> For that I have done RESP charge calculation for my ligand and then have
> created frcmod and lib file for my ligand.
>
> By while generating complex parameter files it is giving me following
> error.
> I am unable to get it why such problem is coming.
> As I am providing it prmtop and lib file of my ligand.
>
> I am attaching the prmtop, lib and pdb file of my ligand so that if any
> one can find my mistake.
>
>
>
> > saveamberparm R_config C8.prmtop C8.inpcrd
> Checking Unit.
> FATAL: Atom .R<UNK 545>.A<C2 1> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H12 2> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H22 3> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C17 4> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H1 5> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H2 6> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C18 7> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C19 8> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C20 9> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C21 10> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C22 11> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C23 12> does not have a type.
> FATAL: Atom .R<UNK 545>.A<N23 13> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C24 14> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H 15> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C26 16> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C28 17> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C27 18> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C29 19> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C25 20> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C30 21> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C31 22> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C33 23> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C32 24> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C35 25> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C36 26> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C34 27> does not have a type.
> FATAL: Atom .R<UNK 545>.A<N36 28> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C37 29> does not have a type.
> FATAL: Atom .R<UNK 545>.A<H3 30> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C 31> does not have a type.
> FATAL: Atom .R<UNK 545>.A<N2 32> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C3 33> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C5 34> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C7 35> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C6 36> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C8 37> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C4 38> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C9 39> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C10 40> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C11 41> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C12 42> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C15 43> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C14 44> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C13 45> does not have a type.
> FATAL: Atom .R<UNK 545>.A<N14 46> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C1 47> does not have a type.
> FATAL: Atom .R<UNK 545>.A<C16 48> does not have a type.
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
> ambermd.org_mailman_listinfo_amber&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=
> 0Hah93XWYYBgmROOVcaccg&m=Phr07uZXjs7d_Lx5hh3p7LNoNoMfhpegEPdT6HRuiCo&s=
> fwQjPsRf57a7cc59Uunmm3caTFRVGJdYyg5kUNgNBOc&e=
>
>
> ------------------------------
>
> Message: 11
> Date: Mon, 1 May 2017 10:59:23 -0400
> From: David Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] does not have a type
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20170501145923.vnjzmvsk3b3udpi6.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Mon, May 01, 2017, Thakur, Abhishek wrote:
>
> > By while generating complex parameter files it is giving me following
> error.
> > FATAL: Atom .R<UNK 545>.A<C2 1> does not have a type.
> > FATAL: Atom .R<UNK 545>.A<H12 2> does not have a type.
>
> Your library file says the unit is "unk", whereas the pdb file has residue
> names of "UNK". These things are case-sensitive: you should edit the
> library file to change unk -> UNK.
>
> ...hope this helps...dac
>
> p.s. if you plan to much of this, pick a different residue name than
> "unknown". Of course, the PDB file and the residue library file still
> have to
> match.
>
>
>
>
> ------------------------------
>
> Message: 12
> Date: Mon, 1 May 2017 11:29:09 -0400
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] Too many iterations in routine! in RMSD
> calculation
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qOZSD+GOr1Lc4MieDXA_7U80qaXcuCp+nr6Eg3DRSyAHBQ.
> mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> On Sat, Apr 29, 2017 at 5:16 AM, kungking Hanpaibool
> <kunkungking.hotmail.com> wrote:
> > When I saw the .log I found
> >
> > ----- 5lrnD_md49.nc (1-200, 1) -----
> > Too many iterations in routine!
> > Convergence failed.
>
> In my experience this either happens when not enough atoms are
> selected (so diagonalization of the covariance matrix fails) or you
> have corrupted coordinates. It would help to see the complete cpptraj
> log - can you send it to me off-list. Thanks,
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
>
>
> ------------------------------
>
> Message: 13
> Date: Mon, 1 May 2017 15:50:42 +0000
> From: kungking Hanpaibool <kunkungking.hotmail.com>
> Subject: Re: [AMBER] Too many iterations in routine! in RMSD
> calculation
> To: AMBER Mailing List <amber.ambermd.org>, "daniel.r.roe.gmail.com"
> <daniel.r.roe.gmail.com>
> Message-ID:
> <MWHPR13MB1216E3E2DF3234E02E7B8CAEA3140.MWHPR13MB1216.
> namprd13.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Dan,
>
>
> The attached file is the cpptraj.out which was generated.
>
> Thank you for your help.
>
>
> Best wishes,
>
> Kungking
>
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Tuesday, May 2, 2017 12:29 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Too many iterations in routine! in RMSD calculation
>
> Hi,
>
> On Sat, Apr 29, 2017 at 5:16 AM, kungking Hanpaibool
> <kunkungking.hotmail.com> wrote:
> > When I saw the .log I found
> >
> > ----- 5lrnD_md49.nc (1-200, 1) -----
> > Too many iterations in routine!
> > Convergence failed.
>
> In my experience this either happens when not enough atoms are
> selected (so diagonalization of the covariance matrix fails) or you
> have corrupted coordinates. It would help to see the complete cpptraj
> log - can you send it to me off-list. Thanks,
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
> The Laboratory of Computational Biology<https://www.lobos.nih.gov/lcb>
> www.lobos.nih.gov
> The Laboratory of Computational Biology is an interdisciplinary group of
> scientists who study biological processes via computer simulation. It is
> part of the ...
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> mailman/listinfo/amber>
> lists.ambermd.org
> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> It is designed to provide a forum for users of the AMBER Molecular Dynamics
> and related ...
>
>
>
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: rmsd_cpptraj_ch.out
> Type: application/octet-stream
> Size: 541812 bytes
> Desc: rmsd_cpptraj_ch.out
> Url : http://lists.ambermd.org/mailman/private/amber/
> attachments/20170501/f800b327/attachment-0001.obj
>
> ------------------------------
>
> Message: 14
> Date: Mon, 1 May 2017 11:55:58 -0400
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] Too many iterations in routine! in RMSD
> calculation
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qOYwem-4VWhgh0ox=KXGSQ1_U-iy06rkFrN7ewOETN4_2w.mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Thanks for the log. Here is your problem:
>
> ```
> 1: [rms reference :326 out ligand_100ns.rms]
> Target mask: [:326](1)
> Reference mask: [:326](1)
> ```
>
> Residue 326 consists of 1 atom. You really need at least 3 atoms for
> an RMSD to make sense (I probably should add a warning about this).
>
> -Dan
>
>
> On Mon, May 1, 2017 at 11:50 AM, kungking Hanpaibool
> <kunkungking.hotmail.com> wrote:
> >
> > Hi Dan,
> >
> >
> > The attached file is the cpptraj.out which was generated.
> >
> > Thank you for your help.
> >
> >
> > Best wishes,
> >
> > Kungking
> >
> >
> >
> > ________________________________
> > From: Daniel Roe <daniel.r.roe.gmail.com>
> > Sent: Tuesday, May 2, 2017 12:29 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Too many iterations in routine! in RMSD calculation
> >
> > Hi,
> >
> > On Sat, Apr 29, 2017 at 5:16 AM, kungking Hanpaibool
> > <kunkungking.hotmail.com> wrote:
> > > When I saw the .log I found
> > >
> > > ----- 5lrnD_md49.nc (1-200, 1) -----
> > > Too many iterations in routine!
> > > Convergence failed.
> >
> > In my experience this either happens when not enough atoms are
> > selected (so diagonalization of the covariance matrix fails) or you
> > have corrupted coordinates. It would help to see the complete cpptraj
> > log - can you send it to me off-list. Thanks,
> >
> > -Dan
> >
> > --
> > -------------------------
> > Daniel R. Roe
> > Laboratory of Computational Biology
> > National Institutes of Health, NHLBI
> > 5635 Fishers Ln, Rm T900
> > Rockville MD, 20852
> > https://www.lobos.nih.gov/lcb
> > The Laboratory of Computational Biology
> > www.lobos.nih.gov
> > The Laboratory of Computational Biology is an interdisciplinary group of
> scientists who study biological processes via computer simulation. It is
> part of the ...
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> > AMBER -- AMBER Mailing List
> > lists.ambermd.org
> > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> It is designed to provide a forum for users of the AMBER Molecular Dynamics
> and related ...
> >
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
>
>
> ------------------------------
>
> Message: 15
> Date: Mon, 1 May 2017 15:59:59 +0000
> From: kungking Hanpaibool <kunkungking.hotmail.com>
> Subject: Re: [AMBER] Too many iterations in routine! in RMSD
> calculation
> To: AMBER Mailing List <amber.ambermd.org>, 'Daniel Roe'
> <daniel.r.roe.gmail.com>
> Message-ID:
> <MWHPR13MB12164D99DA3823CD712ED4B5A3140.MWHPR13MB1216.
> namprd13.prod.outlook.com>
>
> Content-Type: text/plain; charset="windows-874"
>
> ?Hi Dan,
>
>
> I see, Thank you very much for your help.
>
>
> Best regards,
> Kungking
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Tuesday, May 2, 2017 12:55 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Too many iterations in routine! in RMSD calculation
>
> Hi,
>
> Thanks for the log. Here is your problem:
>
> ```
> 1: [rms reference :326 out ligand_100ns.rms]
> Target mask: [:326](1)
> Reference mask: [:326](1)
> ```
>
> Residue 326 consists of 1 atom. You really need at least 3 atoms for
> an RMSD to make sense (I probably should add a warning about this).
>
> -Dan
>
>
> On Mon, May 1, 2017 at 11:50 AM, kungking Hanpaibool
> <kunkungking.hotmail.com> wrote:
> >
> > Hi Dan,
> >
> >
> > The attached file is the cpptraj.out which was generated.
> >
> > Thank you for your help.
> >
> >
> > Best wishes,
> >
> > Kungking
> >
> >
> >
> > ________________________________
> > From: Daniel Roe <daniel.r.roe.gmail.com>
> > Sent: Tuesday, May 2, 2017 12:29 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Too many iterations in routine! in RMSD calculation
> >
> > Hi,
> >
> > On Sat, Apr 29, 2017 at 5:16 AM, kungking Hanpaibool
> > <kunkungking.hotmail.com> wrote:
> > > When I saw the .log I found
> > >
> > > ----- 5lrnD_md49.nc (1-200, 1) -----
> > > Too many iterations in routine!
> > > Convergence failed.
> >
> > In my experience this either happens when not enough atoms are
> > selected (so diagonalization of the covariance matrix fails) or you
> > have corrupted coordinates. It would help to see the complete cpptraj
> > log - can you send it to me off-list. Thanks,
> >
> > -Dan
> >
> > --
> > -------------------------
> > Daniel R. Roe
> > Laboratory of Computational Biology
> > National Institutes of Health, NHLBI
> > 5635 Fishers Ln, Rm T900
> > Rockville MD, 20852
> > https://www.lobos.nih.gov/lcb
> The Laboratory of Computational Biology<https://www.lobos.nih.gov/lcb>
> www.lobos.nih.gov
> The Laboratory of Computational Biology is an interdisciplinary group of
> scientists who study biological processes via computer simulation. It is
> part of the ...
>
>
>
> > The Laboratory of Computational Biology
> > www.lobos.nih.gov<http://www.lobos.nih.gov>
> The Laboratory of Computational Biology<http://www.lobos.nih.gov/>
> www.lobos.nih.gov
> Website of the Laboratory of Computational Biology NHLBI NIH
>
>
>
> > The Laboratory of Computational Biology is an interdisciplinary group of
> scientists who study biological processes via computer simulation. It is
> part of the ...
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> mailman/listinfo/amber>
> lists.ambermd.org
> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> It is designed to provide a forum for users of the AMBER Molecular Dynamics
> and related ...
>
>
>
> > AMBER -- AMBER Mailing List
> > lists.ambermd.org
> > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> It is designed to provide a forum for users of the AMBER Molecular Dynamics
> and related ...
> >
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
> The Laboratory of Computational Biology<https://www.lobos.nih.gov/lcb>
> www.lobos.nih.gov
> The Laboratory of Computational Biology is an interdisciplinary group of
> scientists who study biological processes via computer simulation. It is
> part of the ...
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> mailman/listinfo/amber>
> lists.ambermd.org
> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> It is designed to provide a forum for users of the AMBER Molecular Dynamics
> and related ...
>
>
>
>
>
> ------------------------------
>
> Message: 16
> Date: Mon, 1 May 2017 16:09:42 +0000
> From: kungking Hanpaibool <kunkungking.hotmail.com>
> Subject: Re: [AMBER] Too many iterations in routine! in RMSD
> calculation
> To: AMBER Mailing List <amber.ambermd.org>, 'Daniel Roe'
> <daniel.r.roe.gmail.com>
> Message-ID:
> <MWHPR13MB1216A56D954D134DB3D51AEEA3140.MWHPR13MB1216.
> namprd13.prod.outlook.com>
>
> Content-Type: text/plain; charset="windows-874"
>
> Hi Dan,
>
>
> I also have another question.
>
> Rmsd calculation for protein backbone, The result showed all of frame got
> 0.000.
>
> Why didn't I got the result for backbone?
>
>
> Best regards,
>
> Kungking
>
>
> ________________________________
> From: kungking Hanpaibool <kunkungking.hotmail.com>
> Sent: Tuesday, May 2, 2017 12:59 AM
> To: AMBER Mailing List; 'Daniel Roe'
> Subject: Re: [AMBER] Too many iterations in routine! in RMSD calculation
>
> ?Hi Dan,
>
>
> I see, Thank you very much for your help.
>
>
> Best regards,
> Kungking
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Tuesday, May 2, 2017 12:55 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Too many iterations in routine! in RMSD calculation
>
> Hi,
>
> Thanks for the log. Here is your problem:
>
> ```
> 1: [rms reference :326 out ligand_100ns.rms]
> Target mask: [:326](1)
> Reference mask: [:326](1)
> ```
>
> Residue 326 consists of 1 atom. You really need at least 3 atoms for
> an RMSD to make sense (I probably should add a warning about this).
>
> -Dan
>
>
> On Mon, May 1, 2017 at 11:50 AM, kungking Hanpaibool
> <kunkungking.hotmail.com> wrote:
> >
> > Hi Dan,
> >
> >
> > The attached file is the cpptraj.out which was generated.
> >
> > Thank you for your help.
> >
> >
> > Best wishes,
> >
> > Kungking
> >
> >
> >
> > ________________________________
> > From: Daniel Roe <daniel.r.roe.gmail.com>
> > Sent: Tuesday, May 2, 2017 12:29 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Too many iterations in routine! in RMSD calculation
> >
> > Hi,
> >
> > On Sat, Apr 29, 2017 at 5:16 AM, kungking Hanpaibool
> > <kunkungking.hotmail.com> wrote:
> > > When I saw the .log I found
> > >
> > > ----- 5lrnD_md49.nc (1-200, 1) -----
> > > Too many iterations in routine!
> > > Convergence failed.
> >
> > In my experience this either happens when not enough atoms are
> > selected (so diagonalization of the covariance matrix fails) or you
> > have corrupted coordinates. It would help to see the complete cpptraj
> > log - can you send it to me off-list. Thanks,
> >
> > -Dan
> >
> > --
> > -------------------------
> > Daniel R. Roe
> > Laboratory of Computational Biology
> > National Institutes of Health, NHLBI
> > 5635 Fishers Ln, Rm T900
> > Rockville MD, 20852
> > https://www.lobos.nih.gov/lcb
> The Laboratory of Computational Biology<https://www.lobos.nih.gov/lcb>
> www.lobos.nih.gov
> The Laboratory of Computational Biology is an interdisciplinary group of
> scientists who study biological processes via computer simulation. It is
> part of the ...
>
>
>
> The Laboratory of Computational Biology<https://www.lobos.nih.gov/lcb>
> The Laboratory of Computational Biology<https://www.lobos.nih.gov/lcb>
> www.lobos.nih.gov
> The Laboratory of Computational Biology is an interdisciplinary group of
> scientists who study biological processes via computer simulation. It is
> part of the ...
>
>
>
> www.lobos.nih.gov<http://www.lobos.nih.gov>
> The Laboratory of Computational Biology<http://www.lobos.nih.gov/>
> www.lobos.nih.gov
> Website of the Laboratory of Computational Biology NHLBI NIH
>
>
>
> The Laboratory of Computational Biology is an interdisciplinary group of
> scientists who study biological processes via computer simulation. It is
> part of the ...
>
>
>
> > The Laboratory of Computational Biology
> > www.lobos.nih.gov<http://www.lobos.nih.gov>
> The Laboratory of Computational Biology<http://www.lobos.nih.gov/>
> www.lobos.nih.gov
> Website of the Laboratory of Computational Biology NHLBI NIH
>
>
>
> The Laboratory of Computational Biology<http://www.lobos.nih.gov/>
> The Laboratory of Computational Biology<http://www.lobos.nih.gov/>
> www.lobos.nih.gov
> Website of the Laboratory of Computational Biology NHLBI NIH
>
>
>
> www.lobos.nih.gov<http://www.lobos.nih.gov>
> The Laboratory of Computational Biology<http://www.lobos.nih.gov/>
> www.lobos.nih.gov
> Website of the Laboratory of Computational Biology NHLBI NIH
>
>
>
> Website of the Laboratory of Computational Biology NHLBI NIH
>
>
>
> > The Laboratory of Computational Biology is an interdisciplinary group of
> scientists who study biological processes via computer simulation. It is
> part of the ...
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> mailman/listinfo/amber>
> lists.ambermd.org
> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> It is designed to provide a forum for users of the AMBER Molecular Dynamics
> and related ...
>
>
>
> AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> mailman/listinfo/amber>
> AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> mailman/listinfo/amber>
> lists.ambermd.org
> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> It is designed to provide a forum for users of the AMBER Molecular Dynamics
> and related ...
>
>
>
> lists.ambermd.org
> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> It is designed to provide a forum for users of the AMBER Molecular Dynamics
> and related ...
>
>
>
> > AMBER -- AMBER Mailing List
> > lists.ambermd.org
> > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> It is designed to provide a forum for users of the AMBER Molecular Dynamics
> and related ...
> >
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
> The Laboratory of Computational Biology<https://www.lobos.nih.gov/lcb>
> www.lobos.nih.gov
> The Laboratory of Computational Biology is an interdisciplinary group of
> scientists who study biological processes via computer simulation. It is
> part of the ...
>
>
>
> The Laboratory of Computational Biology<https://www.lobos.nih.gov/lcb>
> The Laboratory of Computational Biology<https://www.lobos.nih.gov/lcb>
> www.lobos.nih.gov
> The Laboratory of Computational Biology is an interdisciplinary group of
> scientists who study biological processes via computer simulation. It is
> part of the ...
>
>
>
> www.lobos.nih.gov<http://www.lobos.nih.gov>
> The Laboratory of Computational Biology<http://www.lobos.nih.gov/>
> www.lobos.nih.gov
> Website of the Laboratory of Computational Biology NHLBI NIH
>
>
>
> The Laboratory of Computational Biology is an interdisciplinary group of
> scientists who study biological processes via computer simulation. It is
> part of the ...
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> mailman/listinfo/amber>
> lists.ambermd.org
> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> It is designed to provide a forum for users of the AMBER Molecular Dynamics
> and related ...
>
>
>
> AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> mailman/listinfo/amber>
> AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> mailman/listinfo/amber>
> lists.ambermd.org
> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> It is designed to provide a forum for users of the AMBER Molecular Dynamics
> and related ...
>
>
>
> lists.ambermd.org
> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> It is designed to provide a forum for users of the AMBER Molecular Dynamics
> and related ...
>
>
>
>
>
> ------------------------------
>
> Message: 17
> Date: Mon, 1 May 2017 16:10:04 +0000
> From: Ramin Salimi <ramin.salimi01.utrgv.edu>
> Subject: Re: [AMBER] Restraint in Steered MD/Jarzynski method
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CY1PR0501MB178803C201C2B292EDD98C2487140.CY1PR0501MB1788.
> namprd05.prod.outlook.com>
>
> Content-Type: text/plain; charset="windows-1256"
>
> Hi Hannes
> Thank you so much for your help.
> Kind Regards
> Ramin
>
> Sent from my Windows Phone
> ________________________________
> From: Hannes Loeffler<mailto:Hannes.Loeffler.stfc.ac.uk>
> Sent: ?5/?1/?2017 2:11 AM
> To: amber.ambermd.org<mailto:amber.ambermd.org>
> Subject: Re: [AMBER] Restraint in Steered MD/Jarzynski method
>
> On Sun, 30 Apr 2017 18:41:18 +0000
> Ramin Salimi <ramin.salimi01.utrgv.edu> wrote:
>
> > Hi Hannes
> >
> > Thanks so very much for the reply because I really need clarification.
> >
> > Regarding the first question, I am confused between either one of
> > these two:
> >
> > 1- minimize, heat up, equilibration. Then pick 'n' frames from the
> > equilibration trajectory, and do SMD on each
>
> The Jarzynski method requires you to start from equilibrated initial
> states. So if you run N non-equilibrium simulations you will need N
> such states. These states should be unbiased (so not restraints),
> independent from each other and representative for the state you start
> from.
>
>
> Cheers,
> Hannes.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://na01.safelinks.protection.outlook.com/?url=
> http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%
> 2Famber&data=02%7C01%7Cramin.salimi01%40utrgv.edu%
> 7C9ddbf26176cf415aa9e508d490615995%7C990436a687df491c91249afa91f8
> 8827%7C0%7C0%7C636292195174550575&sdata=5ZnEqd1XwJ7Qcpt5PKtxg%
> 2B5C6KO6p06jnRwneFJ9sXM%3D&reserved=0
>
>
> ------------------------------
>
> Message: 18
> Date: Mon, 1 May 2017 12:23:09 -0400
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] Too many iterations in routine! in RMSD
> calculation
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qOZACpwR06G6KMB34U_Ef_0nm_SJx=wNqVt0y-dCrbPcmg.mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Mon, May 1, 2017 at 12:09 PM, kungking Hanpaibool
> <kunkungking.hotmail.com> wrote:
> >
> > Rmsd calculation for protein backbone, The result showed all of frame got
> > 0.000.
> >
> > Why didn't I got the result for backbone?
>
> Difficult to say without seeing the original data. Have you tried
> visualizing the trajectory data? I suppose it's possible that the RMSD
> to your reference is smaller than the printed precision but that seems
> unlikely.
>
> If there is something weird with your unit cell (e.g. from a prior
> coordinate rotation with 'rms') it's possible the imaging is resulting
> in bad coordinates. You could take away the 'autoimage' command to
> check for this.
>
> -Dan
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
>
>
> ------------------------------
>
> Message: 19
> Date: Mon, 1 May 2017 17:50:48 +0000
> From: Ramin Salimi <ramin.salimi01.utrgv.edu>
> Subject: [AMBER] Find entropy from non-equilibrium free energy
> calculation
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID:
> <CY1PR0501MB1788B88C475F5A7B4FD3C78587140.CY1PR0501MB1788.
> namprd05.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear All
>
> I have two questions regarding non-equilibrium free energy calculation:
>
>
> --Given that we calculate PMF(Free energy difference) from Jarzynski
> equality, How can we get the entropy (difference) from that? By entropy, I
> mean configurational entropic change?
>
> -- How should I check the standard deviation to see if the free energy I
> have gotten through Jarzynski equality is more than a few KBT or not? Is
> there any way to check the free energy accuracy? And how can I make sure
> that this 'n' number of structures I picked is enough for sampling or I
> need more than 'n' numbers?
>
>
> Thanks in Advance
>
> Ramin
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 1921, Issue 1
> **************************************
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 10 2017 - 22:00:02 PDT
