My water residue is named "TIP3". I have tried adding the following lines
in my AMBER input
jfastw=1,
WATNAM="TIP3",
OWTNM="OH2",
HWTNM1="H1"
HWTNM2="H2"
But that hasn't helped. I also just tried renaming the water residues to
"WAT", which is AMBER default, but the error persists.
Chitrak.
On Sat, Oct 3, 2015 at 3:00 PM, <amber-request.ambermd.org> wrote:
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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: ^.^. as a new atom type when running DFTB with sander
> from Ambertools 15 (Gustavo Seabra)
> 2. problem with randomizing velocities
> (Kalenkiewicz, Andrew (NIH/NICHD) [F])
> 3. Re: problem with randomizing velocities (Bill Ross)
> 4. Re: problem with randomizing velocities (Bill Ross)
> 5. TIP3 water not recognized (Chitrak Gupta)
> 6. Re: TIP3 water not recognized (Bill Ross)
> 7. Re: problem with randomizing velocities (Hector A. Baldoni)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 2 Oct 2015 16:51:29 -0300
> From: Gustavo Seabra <gustavo.seabra.gmail.com>
> Subject: Re: [AMBER] ^.^. as a new atom type when running DFTB with
> sander from Ambertools 15
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <540D0CCC-8E70-4A04-92FF-ECD3893F1B1A.gmail.com>
> Content-Type: text/plain; charset=utf-8
>
> Hi Emilio,
>
> That shouldn?t happen, and it looks more like a case of corrupted file
> somehow. Can you send me input input files so I can try them?
>
> Gustavo Seabra
>
>
>
> > Em 02/10/2015, ?(s) 15:11, Emilio Lence <guitarro.de.meixente.gmail.com>
> escreveu:
> >
> > Dear amber users
> > Recently I installed the AmberTools 15. When I tried to run a DFTB
> > calculation with sander module, I couldn't. The reason is that do not
> > recognised some atoms. In my case were 3 O atoms are recognised not as
> > oxygen but as ^.^.. As a consequence I have an additional atom type (7
> > instead of 6) with no parameters for it. I tried to copy de O-X.skf files
> > as ^.^.-X.skf, but the sander module do not recognised the new files
> > (although it ask for then). In previous versions of amber, you can run
> the
> > job without problem.
> > I'm almost sure that I installed all the updates fro ambertools, but
> right
> > now I can't access the website of amber to check if there is son update
> > related with this problem.
> > Thanks for your kind attention
> > Have a nice weekend
> >
> >
> > --
> > Dr. Emilio Lence Quintana
> > Organic Chemistry Department-CIQUS
> > University of Santiago de Compostela
> > 15782 Santiago de Compostela, Spain
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 2 Oct 2015 20:58:55 +0000
> From: "Kalenkiewicz, Andrew (NIH/NICHD) [F]"
> <andrew.kalenkiewicz.nih.gov>
> Subject: [AMBER] problem with randomizing velocities
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID: <DDEBFE0D6BC5B94BB27C05168B7A2DC06F28DF.msgb08.nih.gov>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Amber users,
>
> I am trying to start an accelerated MD simulation from an equilibrated
> system using a random seed (ig=-1) for the velocities, but for some reason
> there is a large temperature spike at the beginning of my simulation when I
> use the following input file:
>
> molecular dynamics run
> &cntrl
> imin=0, irest=0, ntx=1,
> ntt=3, tempi=300.0, gamma_ln=2.0,
> ig=-1, ntp=0, ntb=1, ntc=2, ntf=2,
> cut=10.0, nsnb=20, dt=0.002,
> nstlim=2500000, ioutfm=1,
> ntwe=200, ntwx=200, ntpr=50,
> iamd=3,
> EthreshD = 14744.2984, alphaD = 606.2,
> EthreshP = -365669.03, alphaP = 25317.8,
> &end
>
> The temperature starts at ~430K, drops to around 270K, and then
> equilibrates to 300K. But according to the manual:
>
> "For the initial dynamics run, (NTX .lt. 3) the velocities are assigned
> from a
> Maxwellian distribution at TEMPI K."
>
> Therefore why isn't the initial temperature at my specified value of 300K?
>
> Thanks,
> Andrew
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 2 Oct 2015 14:05:39 -0700
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] problem with randomizing velocities
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <560EF1A3.7030203.cgl.ucsf.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> You are jump-starting an unequilibrated block of ice to 300K. Short
> answer is restrain your solute at first or warm gradually.
>
> Bill
>
> On 10/2/2015 1:58 PM, Kalenkiewicz, Andrew (NIH/NICHD) [F] wrote:
> > Dear Amber users,
> >
> > I am trying to start an accelerated MD simulation from an equilibrated
> system using a random seed (ig=-1) for the velocities, but for some reason
> there is a large temperature spike at the beginning of my simulation when I
> use the following input file:
> >
> > molecular dynamics run
> > &cntrl
> > imin=0, irest=0, ntx=1,
> > ntt=3, tempi=300.0, gamma_ln=2.0,
> > ig=-1, ntp=0, ntb=1, ntc=2, ntf=2,
> > cut=10.0, nsnb=20, dt=0.002,
> > nstlim=2500000, ioutfm=1,
> > ntwe=200, ntwx=200, ntpr=50,
> > iamd=3,
> > EthreshD = 14744.2984, alphaD = 606.2,
> > EthreshP = -365669.03, alphaP = 25317.8,
> > &end
> >
> > The temperature starts at ~430K, drops to around 270K, and then
> equilibrates to 300K. But according to the manual:
> >
> > "For the initial dynamics run, (NTX .lt. 3) the velocities are assigned
> from a
> > Maxwellian distribution at TEMPI K."
> >
> > Therefore why isn't the initial temperature at my specified value of
> 300K?
> >
> > Thanks,
> > Andrew
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 2 Oct 2015 14:12:11 -0700
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] problem with randomizing velocities
> To: amber.ambermd.org
> Message-ID: <560EF32B.90300.cgl.ucsf.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> I misspoke about unequilibrated, but even being equilibrated, the system
> will have a sudden jump in temperature that reflects how the random
> velocities interact with the force field.
>
> Bill
>
> On 10/2/2015 2:05 PM, Bill Ross wrote:
> > You are jump-starting an unequilibrated block of ice to 300K. Short
> > answer is restrain your solute at first or warm gradually.
> >
> > Bill
> >
> > On 10/2/2015 1:58 PM, Kalenkiewicz, Andrew (NIH/NICHD) [F] wrote:
> >> Dear Amber users,
> >>
> >> I am trying to start an accelerated MD simulation from an equilibrated
> system using a random seed (ig=-1) for the velocities, but for some reason
> there is a large temperature spike at the beginning of my simulation when I
> use the following input file:
> >>
> >> molecular dynamics run
> >> &cntrl
> >> imin=0, irest=0, ntx=1,
> >> ntt=3, tempi=300.0, gamma_ln=2.0,
> >> ig=-1, ntp=0, ntb=1, ntc=2, ntf=2,
> >> cut=10.0, nsnb=20, dt=0.002,
> >> nstlim=2500000, ioutfm=1,
> >> ntwe=200, ntwx=200, ntpr=50,
> >> iamd=3,
> >> EthreshD = 14744.2984, alphaD = 606.2,
> >> EthreshP = -365669.03, alphaP = 25317.8,
> >> &end
> >>
> >> The temperature starts at ~430K, drops to around 270K, and then
> equilibrates to 300K. But according to the manual:
> >>
> >> "For the initial dynamics run, (NTX .lt. 3) the velocities are assigned
> from a
> >> Maxwellian distribution at TEMPI K."
> >>
> >> Therefore why isn't the initial temperature at my specified value of
> 300K?
> >>
> >> Thanks,
> >> Andrew
> >> _______________________________________________
> >> 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
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 2 Oct 2015 19:03:35 -0400
> From: Chitrak Gupta <chgupta.mix.wvu.edu>
> Subject: [AMBER] TIP3 water not recognized
> To: amber.ambermd.org
> Message-ID:
> <CANWBmSuXkP9AD4obs=
> mDrfSzexxxPs7y4Pc2Uifuh-GoaeeU+A.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> I am trying to use chamber 14 to generate AMBER inputs. I am using xplor
> extended formatted PSF file for this. chamber runs fine, but when I try to
> run AMBER (pmemd.cuda version), I am getting the following error:
>
> Hydrogen atom 26802 appears to have multiple bonds to atoms 26801 and 26803
> which is illegal for SHAKEH.
> Exiting due to the presence of inconsistent SHAKEH hydrogen clusters.
>
>
> My system has protein, lipid and waters, and the pdb/psf files were
> generated by charmm-gui.org
>
> Does anyone know how I could fix this?
>
>
>
> Regards,
> Chitrak.
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 02 Oct 2015 18:04:57 -0700
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] TIP3 water not recognized
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <ob2xed65pnm92mo4njrnnfna.1443834297968.email.android.com>
> Content-Type: text/plain; charset=utf-8
>
> Sounds like the water residue name is not being mapped to the
> triangular-bond TIP3 model. What is your water residue name?
>
> Bill
>
> <div>-------- Original message --------</div><div>From: Chitrak Gupta <
> chgupta.mix.wvu.edu> </div><div>Date:10/02/2015 4:03 PM (GMT-08:00)
> </div><div>To: amber.ambermd.org </div><div>Subject: [AMBER] TIP3 water
> not recognized </div><div>
> </div>Hi,
>
> I am trying to use chamber 14 to generate AMBER inputs. I am using xplor
> extended formatted PSF file for this. chamber runs fine, but when I try to
> run AMBER (pmemd.cuda version), I am getting the following error:
>
> Hydrogen atom 26802 appears to have multiple bonds to atoms 26801 and 26803
> which is illegal for SHAKEH.
> Exiting due to the presence of inconsistent SHAKEH hydrogen clusters.
>
>
> My system has protein, lipid and waters, and the pdb/psf files were
> generated by charmm-gui.org
>
> Does anyone know how I could fix this?
>
>
>
> Regards,
> Chitrak.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> ------------------------------
>
> Message: 7
> Date: Sat, 3 Oct 2015 01:14:09 -0300 (ARGSL-ST)
> From: "Hector A. Baldoni" <hbaldoni.unsl.edu.ar>
> Subject: Re: [AMBER] problem with randomizing velocities
> To: "AMBER Mailing List" <amber.ambermd.org>
> Message-ID:
> <1942.190.6.211.31.1443845649.squirrel.webmail.unsl.edu.ar>
> Content-Type: text/plain;charset=iso-8859-1
>
> Hi,
>
> Try to restart each run adding TEMP0=300, IREST=1,
>
> Greeting,
> Hector.
>
>
> > Dear Amber users,
> >
> > I am trying to start an accelerated MD simulation from an equilibrated
> > system using a random seed (ig=-1) for the velocities, but for some
> reason
> > there is a large temperature spike at the beginning of my simulation when
> > I use the following input file:
> >
> > molecular dynamics run
> > &cntrl
> > imin=0, irest=0, ntx=1,
> > ntt=3, tempi=300.0, gamma_ln=2.0,
> > ig=-1, ntp=0, ntb=1, ntc=2, ntf=2,
> > cut=10.0, nsnb=20, dt=0.002,
> > nstlim=2500000, ioutfm=1,
> > ntwe=200, ntwx=200, ntpr=50,
> > iamd=3,
> > EthreshD = 14744.2984, alphaD = 606.2,
> > EthreshP = -365669.03, alphaP = 25317.8,
> > &end
> >
> > The temperature starts at ~430K, drops to around 270K, and then
> > equilibrates to 300K. But according to the manual:
> >
> > "For the initial dynamics run, (NTX .lt. 3) the velocities are assigned
> > from a
> > Maxwellian distribution at TEMPI K."
> >
> > Therefore why isn't the initial temperature at my specified value of
> 300K?
> >
> > Thanks,
> > Andrew
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --------------------------------------
> Dr. H?ctor A. Baldoni
> Departamento de Qu?mica
> ?rea de Qu?mica General e Inorg?nica
> Universidad Nacional de San Luis
> Chacabuco 917 (D5700BWS)
> San Luis - Argentina
> hbaldoni at unsl dot edu dot ar
> Tel.:+54-(0)266-4520300 ext. 6157
> --------------------------------------
>
>
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 1361, Issue 1
> **************************************
>
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Received on Sun Oct 04 2015 - 11:30:04 PDT
