Dear Sir,
I added the "loadOff terminal_monophosphate.lib" as per your suggestion,
yet find the same error for 805 residue only. Then, I replaced U with OHE
and it worked.
Thanks a lot Sir.
On Sat, Mar 13, 2021 at 1:34 AM <amber-request.ambermd.org> wrote:
> Send AMBER mailing list submissions to
> amber.ambermd.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.ambermd.org/mailman/listinfo/amber
> or, via email, send a message with subject or body 'help' to
> amber-request.ambermd.org
>
> You can reach the person managing the list at
> amber-owner.ambermd.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of AMBER digest..."
>
>
> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: Problem with CG minimization in implicit solvent
> (David A Case)
> 2. Re: Problem with CG minimization in implicit solvent
> (Alejandro Gil Ley)
> 3. Why a target ion failed to move along the pathway in the
> simulated annealing version of Nudged Elastic Band (NEB)
> calculations? (Li Dailin)
> 4. Re: Problem with CG minimization in implicit solvent (Chris Neale)
> 5. Error in tleap (richa anand)
> 6. Tleap Fatal error (richa anand)
> 7. Re: Tleap Fatal error (David A Case)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 11 Mar 2021 16:18:35 -0500
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Problem with CG minimization in implicit solvent
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <20210311211835.aaz7uwbolcthriwd.sas-cnu404c7j4.rad.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Thu, Mar 11, 2021, Adrian Roitberg wrote:
>
> >> After the first initial steps using steepest descent, CG energies and
> >> forces exhibited frequent jumps of several orders of magnitude as the
> >> minimization progressed.
>
> But it looks like you are still getting lower energies.
>
> FWIW: the conjugate gradient code in runmin is about the oldest code
> around in Amber: I think it even precedes molecular dynamics. The entire
> runmin subroutine will be gone from future releases of sander, but not for
> AmberTools21. I don't know how we will handle the situation for
> pmemd.cuda.
>
> >> If the xmin minimizer is used with PRCG then the issue disappears.
>
> Indeed. Anyone who wants a good minimization should use xmin; just be sure
> to turn off SHAKE. (The latter is done automatically in development
> codes.)
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 11 Mar 2021 21:56:26 +0000
> From: Alejandro Gil Ley <alejandro.gilley.zymeworks.com>
> Subject: Re: [AMBER] Problem with CG minimization in implicit solvent
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <44CCECDD-01CC-4EA5-B3F9-F5D125CB5019.zymeworks.com>
> Content-Type: text/plain; charset="utf-8"
>
> Thank you very much Prof. Roitberg and Prof. Case for your quick replies.
> I appreciate you taking the time to reproduce this issue and providing
> such a detailed answer.
>
> Thanks,
> Alejandro
>
>
> ?On 2021-03-11, 1:18 PM, "David A Case" <david.case.rutgers.edu> wrote:
>
> This email originated outside of Zymeworks
> ________________________________
>
> On Thu, Mar 11, 2021, Adrian Roitberg wrote:
>
> >> After the first initial steps using steepest descent, CG energies
> and
> >> forces exhibited frequent jumps of several orders of magnitude as
> the
> >> minimization progressed.
>
> But it looks like you are still getting lower energies.
>
> FWIW: the conjugate gradient code in runmin is about the oldest code
> around in Amber: I think it even precedes molecular dynamics. The
> entire
> runmin subroutine will be gone from future releases of sander, but not
> for
> AmberTools21. I don't know how we will handle the situation for
> pmemd.cuda.
>
> >> If the xmin minimizer is used with PRCG then the issue disappears.
>
> Indeed. Anyone who wants a good minimization should use xmin; just be
> sure
> to turn off SHAKE. (The latter is done automatically in development
> codes.)
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
>
> https://protect2.fireeye.com/v1/url?k=7a8e5af1-251563f4-7a894f2c-86a279d0e4b2-1e0bfaf71b665eb3&q=1&e=fa12dc7c-98e4-488c-a0fb-f074fa3884bd&u=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber
>
> Notice of Confidentiality: The information transmitted is intended only
> for the person or entity to which it is addressed and may contain
> confidential and/or privileged material. Any review, re-transmission,
> dissemination or other use of or taking of any action in reliance upon this
> information by persons or entities other than the intended recipient is
> prohibited. If you received this in error please contact the sender
> immediately by return electronic transmission and then immediately delete
> this transmission including all attachments without copying, distributing
> or disclosing the same.
>
> ------------------------------
>
> Message: 3
> Date: Fri, 12 Mar 2021 01:55:57 +0000
> From: Li Dailin <lidl25.hotmail.com>
> Subject: [AMBER] Why a target ion failed to move along the pathway in
> the simulated annealing version of Nudged Elastic Band (NEB)
> calculations?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> ME3P282MB20494BD93DAF7E0C55357731C56F9.ME3P282MB2049.AUSP282.PROD.OUTLOOK.COM
> >
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> I intend to pull a K+ ion to move along an ion channel (more than 1000
> amino residues) in the simulated annealing version of NEB simulations
> (Amber18), based on the Amber Tutorial 6.6. The jobs could finish normally,
> however, the target K+ ion did not move and just stayed as in the double
> end points (initial and final structures) throughout the simulation stages
> (heating, equilibrating, simulated annealing, ...), no matter how large the
> pulling force is (skmin/skmax = 10 ~ 5000). The input and output files of
> the equilibration stage are listed below.
>
> Input file (equilibration stage):
>
> &cntrl
> Imin = 0, irest = 1, ntx = 5, igb = 1, ntb = 0, cut = 999, ntc = 2, ntf =
> 2,
> Ntt = 3, gamma_ln = 1000.0, saltcon = 0.2,
> Nstlim = 500000, dt = 0.002, ioutfm = 1, ntxo = 2,
> Ntpr = 5000, ntwx = 50000, ntwr = 50000, ig = -1,
> temp0 = 300.0,
> tgtfitmask = ":1318",
> tgtrmsmask = ":1318", (# The residue 1318 is the target K+ ion)
> ineb = 1, skmin = 5000, skmax = 5000,
> /
>
> Output file (the last step and averages):
>
> NSTEP = 500000 TIME(PS) = 1200.000 TEMP(K) = 303.52 PRESS =
> 0.0
> Etot = -19202.5394 EKtot = 16391.3086 EPtot = -35593.8480
> BOND = 4266.3934 ANGLE = 10950.4327 DIHED = 17323.5818
> 1-4 NB = 4964.0690 1-4 EEL = 53531.0571 VDWAALS = -11263.2521
> EELEC= -95209.5891 EGB = -20156.5407 RESTRAINT = 0.0000
> NEB replicate breakdown:
> Energy for replicate 1 = -51475.5670
> Energy for replicate 2 = -35441.3415
> Energy for replicate 3 = -35478.5552
> Energy for replicate 4 = -35444.8940
> Energy for replicate 5 = -35541.9040
> Energy for replicate 6 = -35304.6905
> Energy for replicate 7 = -35430.2560
> Energy for replicate 8 = -35298.4472
> Energy for replicate 9 = -35593.8480
> Energy for replicate 10 = -51365.6858
> Total Energy of replicates = -386375.1892
>
> ------------------------------------------------------------------------------
> A V E R A G E S O V E R 100 S T E P S
>
> NSTEP = 500000 TIME(PS) = 1200.000 TEMP(K) = 299.83 PRESS =
> 0.0
> Etot = -19241.8113 EKtot = 16192.1339 EPtot =
> -35433.9452
> BOND = 4292.8217 ANGLE = 11070.3246 DIHED = 17397.3694
> 1-4 NB = 4924.4078 1-4 EEL = 53580.2989 VDWAALS =
> -11299.9451
> EELEC = -95522.7562 EGB = -19876.4662 RESTRAINT =
> 0.0000
> NEB replicate breakdown:
> Energy for replicate 1 = -51475.5670
> Energy for replicate 2 = -35441.3415
> Energy for replicate 3 = -35478.5552
> Energy for replicate 4 = -35444.8940
> Energy for replicate 5 = -35541.9040
> Energy for replicate 6 = -35304.6905
> Energy for replicate 7 = -35430.2560
> Energy for replicate 8 = -35298.4472
> Energy for replicate 9 = -35593.8480
> Energy for replicate 10 = -51365.6858
> Total Energy of replicates = -386375.1892
>
>
> Questions:
>
> (1) What is wrong with the input file? How to pull the target K+ ion along
> the pathway?
>
> (2) The energy in the output file does not look fine. The energies of
> replicate 1 (initial structure) and 10 (final structure) are quite
> different from the other replicas, which is not the same way as the Amber
> Tutorial 6.6. I have double checked the structures from each replica and
> found replicate 1-5 get a similar configuration to the initial structure
> and 6-10 get a similar to the final. Does the energy indicate any problems?
>
> Thank a lot for your help. Looking forward to your reply.
>
> Best,
> Dailin
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 11 Mar 2021 21:33:37 -0700
> From: Chris Neale <candrewn.gmail.com>
> Subject: Re: [AMBER] Problem with CG minimization in implicit solvent
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAOge3zjWts-4H1XdsyQJ_rtHVF74hRxdk8P6fD22ZiM=
> VEQxwQ.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Wild guess: does this code increase the step size without bound every time
> an iteration leads to a lower energy? If so, limiting the max step size
> could be a solution as I've seen this type of algorithm (even in steepest
> descent) lead to pathologies in energy minimization of systems that start
> far enough from a minimum that the step size becomes unwieldy large at some
> point.
>
> On Thu, Mar 11, 2021 at 2:18 PM David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Thu, Mar 11, 2021, Adrian Roitberg wrote:
> >
> > >> After the first initial steps using steepest descent, CG energies and
> > >> forces exhibited frequent jumps of several orders of magnitude as the
> > >> minimization progressed.
> >
> > But it looks like you are still getting lower energies.
> >
> > FWIW: the conjugate gradient code in runmin is about the oldest code
> > around in Amber: I think it even precedes molecular dynamics. The entire
> > runmin subroutine will be gone from future releases of sander, but not
> for
> > AmberTools21. I don't know how we will handle the situation for
> > pmemd.cuda.
> >
> > >> If the xmin minimizer is used with PRCG then the issue disappears.
> >
> > Indeed. Anyone who wants a good minimization should use xmin; just be
> sure
> > to turn off SHAKE. (The latter is done automatically in development
> > codes.)
> >
> > ....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 12 Mar 2021 15:34:28 +0530
> From: richa anand <richaaanand.gmail.com>
> Subject: [AMBER] Error in tleap
> To: amber.ambermd.org
> Message-ID:
> <
> CA+Sg6Q2Sy6QP_4uw2rqfYSV6-aaApEVNRxogcbq0DHsNv+dR+A.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear users,
>
> I am running tleap for siRNA-mRNA-Ago complex using Amber20. But, each time
> I get the following error message,
>
> FATAL: Atom .R<U5 805>.A<OP3 29> does not have a type.
> FATAL: Atom .R<U5 805>.A<P 30> does not have a type.
> FATAL: Atom .R<U5 805>.A<OP1 31> does not have a type.
> FATAL: Atom .R<U5 805>.A<OP2 32> does not have a type.
>
> Regards,
> Richa
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 12 Mar 2021 16:39:37 +0530
> From: richa anand <richaaanand.gmail.com>
> Subject: [AMBER] Tleap Fatal error
> To: amber.ambermd.org
> Message-ID:
> <
> CA+Sg6Q0ap44-WogWKvZzOyGMCgVpe0mjAyqUXc6wJBfO66Tqcg.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Users,
>
> I am using the following input parameters for tleap input. Before it I have
> run pdb4amber also.
>
> Tleap input:
>
> source leaprc.protein.ff14SB
> source leaprc.RNA.OL3
> source leaprc.water.tip3p
> designed = loadPdb 6mdz-R.amber.pdb
> check designed
> addions designed Na+ 8
> solvatebox designed TIP3PBOX 10.00 0.75
> charge designed
> saveAmberParm designed 6mdz-R.amber.prm.top 6mdz-R.amber.prm.crd
> savepdb designed 6mdz-R.amber.out.pdb
> quit
>
>
> After running, Tleap I am getting this error message again and again:
>
> FATAL: Atom .R<U5 805>.A<OP3 29> does not have a type.
> FATAL: Atom .R<U5 805>.A<P 30> does not have a type.
> FATAL: Atom .R<U5 805>.A<OP1 31> does not have a type.
> FATAL: Atom .R<U5 805>.A<OP2 32> does not have a type.
> FATAL: Atom .R<A5 825>.A<P 32> does not have a type.
> FATAL: Atom .R<A5 825>.A<OP1 33> does not have a type.
> FATAL: Atom .R<A5 825>.A<OP2 34> does not have a type.
>
>
> ------------------------------
>
> Message: 7
> Date: Fri, 12 Mar 2021 07:54:30 -0500
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Tleap Fatal error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <20210312125430.22bzavlbmddspccs.sas-cnu404c7j4.rad.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Fri, Mar 12, 2021, richa anand wrote:
> >
> >FATAL: Atom .R<U5 805>.A<OP3 29> does not have a type.
> >FATAL: Atom .R<U5 805>.A<P 30> does not have a type.
> >FATAL: Atom .R<U5 805>.A<OP1 31> does not have a type.
> >FATAL: Atom .R<U5 805>.A<OP2 32> does not have a type.
> >FATAL: Atom .R<A5 825>.A<P 32> does not have a type.
> >FATAL: Atom .R<A5 825>.A<OP1 33> does not have a type.
> >FATAL: Atom .R<A5 825>.A<OP2 34> does not have a type.
>
> Your RNA molecules have terminal monophosphates, which is not the default.
>
> If you are using leaprc.RNA.OL3, just add the following line to your tleap
> script, *after* the "source leaprc.RNA.OL3" command:
>
> loadOff terminal_monophosphate.lib
>
> If you are using leaprc.RNA.LJbb, you should edit your input PDB file, to
> name residues 805 and 825 UMP and AMP, respectively.
>
> (Dan, Christina: the terminal_monophosphate.lib file allows users to avoid
> modifying files that come from the RCSB, where "U" is used for a terminal
> base irrespective of whether it has an attached phosphate or not. On the
> other hand, it fails if some terminal bases have phosphates and others do
> not. Do you have thoughts on which is better?
>
> I'm thinking we should teach pdb4amber to look for this, and automatically
> change U -> UMP, etc. Then have the -bres option in ambpdb do the
> reverse.)
>
> ....dac
>
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 3300, Issue 1
> **************************************
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Mar 13 2021 - 01:00:03 PST
