Hi amber users,
Thank you for your suggestions.
I already have solved the error, but I obtain another one. I added below.
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /opt/amber16/bin/mmpbsa_py_energy
cpptraj found! Using /opt/amber16/bin/cpptraj
Preparing trajectories for simulation...
2000 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /opt/amber16/bin/mmpbsa_py_energy
calculating complex contribution...
File "/opt/amber16/bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa()
File "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line
82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line
431, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /opt/amber16/bin/mmpbsa_py_energy failed with prmtop
protein_dry.prmtop!
PB Bomb in pb_aaradi(): No radius assigned for atom 17 C10 CD
Exiting. All files have been retained.
How can deal with this error?
Thank you in advanced for your help
Sincerely
Tiffani
Perfil público*
https://es.linkedin.com/in/tiffanirovira
<
https://es.linkedin.com/in/tiffanirovira>*
[image: Ver imagen en tamaño completo]
2017-02-20 21:00 GMT+01:00 <amber-request.ambermd.org>:
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>
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of AMBER digest..."
>
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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Distance between of each residues of two chains within
> trajectory (Jesmita Dhar)
> 2. SO4 molecule xleap (ARMIN HODAEI)
> 3. Re: SO4 molecule xleap (Elvis Martis)
> 4. Problem with mmpbsa (Tiffani Rovira)
> 5. Re: Problem with mmpbsa (Elvis Martis)
> 6. Re: Problem with mmpbsa (Bill Ross)
> 7. error in the input file (Michael Shokhen)
> 8. Re: error in the input file (Bill Ross)
> 9. Re: error in the input file (Michael Shokhen)
> 10. Re: error in the input file (Bill Ross)
> 11. Re: error in the input file (Michael Shokhen)
> 12. Re: error in the input file (Bill Ross)
> 13. Re: error in the input file (Michael Shokhen)
> 14. Re: error in the input file (Qinghua Liao)
> 15. Re: error in the input file (Hannes Loeffler)
> 16. Re: error in the input file (Michael Shokhen)
> 17. changing chirality with ParmEd? (Thomas Pochapsky)
> 18. Re: Problem with mmpbsa (David Case)
> 19. Re: Using CHARMM 36 force field in AMBER (Brian Radak)
> 20. Re: LeAP and FFs for Hybrid DNA/RNA structure
> (Kasprzak, Wojciech (NIH/NCI) [C])
> 21. Re: changing chirality with ParmEd? (Hai Nguyen)
> 22. Re: LeAP and FFs for Hybrid DNA/RNA structure (Hai Nguyen)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 20 Feb 2017 14:52:33 +0530
> From: Jesmita Dhar <dhar.beauty.gmail.com>
> Subject: [AMBER] Distance between of each residues of two chains
> within trajectory
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAMS2ayr-+q6-Q=33pbbfF8=GE8nTQNhhmU00OpgPu+c1cRZQXg.mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
> I have simulated two 6 residues long peptides,separated by 2 nm. Now I want
> to study if there is any possibilibity of fibrillation over time. For this,
> I want to find out the closest residues for each of the residues present in
> peptide during the simulation. Is it possible in AMBER or in VMD. Please
> help me..
> --
> -Jesmita Dhar
> Senior Research Fellow
> Bose Institute
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 20 Feb 2017 13:53:06 +0300
> From: ARMIN HODAEI <ahodaei15.ku.edu.tr>
> Subject: [AMBER] SO4 molecule xleap
> To: amber.ambermd.org
> Message-ID:
> <CAE-mGxyHbu7GgMmwhna7-g5qkV4Y+pXc28kUmg68XzFm4rnFbg@
> mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear all,
>
> I want to extract prmtop and inpcrd data from the Solvatebox, but
> AMBER does not identify SO4 molecule. Does anybody knows how can I add this
> molecule to the AMBER xleap?
>
> Armin
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 20 Feb 2017 11:35:02 +0000
> From: "Elvis Martis" <elvis.martis.bcp.edu.in>
> Subject: Re: [AMBER] SO4 molecule xleap
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <PN1PR01MB0830866E4571D4AC067E3243A35E0.PN1PR01MB0830.
> INDPRD01.PROD.OUTLOOK.COM>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> HI,
> You need the parameters for SO4 in order to build the prmtop and inpcrd
> file in leap.
> See this earlier post http://archive.ambermd.org/200501/0128.html
> And this http://www.ccl.net/chemistry/resources/messages/1997/03/28.
> 001-dir/index.html
>
>
> ? ? 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: ARMIN HODAEI [mailto:ahodaei15.ku.edu.tr]
> Sent: Monday, February 20, 2017 4:23 PM
> To: amber.ambermd.org
> Subject: [AMBER] SO4 molecule xleap
>
> Dear all,
>
> I want to extract prmtop and inpcrd data from the Solvatebox, but
> AMBER does not identify SO4 molecule. Does anybody knows how can I add this
> molecule to the AMBER xleap?
>
> Armin
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 20 Feb 2017 13:11:04 +0100
> From: Tiffani Rovira <tiffanirovira.gmail.com>
> Subject: [AMBER] Problem with mmpbsa
> To: amber.ambermd.org
> Message-ID:
> <CAGsoVvmYFVX1r3sWicgKyK7EcevkmbZ4BMeZod7unAWiSdKskA.mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi users,
>
> I have the following problem with the mmpbsa calculation:
>
> Loading and checking parameter files for compatibility...
> File "/opt/amber16/bin/MMPBSA.py", line 98, in <module>
> app.loadcheck_prmtops()
> File "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line
> 572, in loadcheck_prmtops
> FILES.receptor_prmtop, FILES.ligand_prmtop)
> File
> "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py", line
> 109, in __init__
> self._validate()
> File
> "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py", line
> 876, in _validate
> raise PrmtopError('Complex natom != receptor natom + ligand natom')
> PrmtopError: Complex natom != receptor natom + ligand natom
> Exiting. All files have been retained.
>
> I already have tried to solve it but I couldn't.
>
> How can deal with this problem?
>
> Sincerely
>
> Tiffany
> Perfil p?blico*https://es.linkedin.com/in/tiffanirovira
> <https://es.linkedin.com/in/tiffanirovira>*
> [image: Ver imagen en tama?o completo]
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 20 Feb 2017 12:15:15 +0000
> From: "Elvis Martis" <elvis.martis.bcp.edu.in>
> Subject: Re: [AMBER] Problem with mmpbsa
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <PN1PR01MB08308AFC71530443186E5992A35E0.PN1PR01MB0830.
> INDPRD01.PROD.OUTLOOK.COM>
>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
> Have you set the environments correctly?
> Try to run this command before running mmpbsa
> Source $AMBERHOME/amber.sh (bash)
> Or
> Source $AMBERHOME/amber.csh (csh)
>
> ? ? 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: Tiffani Rovira [mailto:tiffanirovira.gmail.com]
> Sent: Monday, February 20, 2017 5:41 PM
> To: amber.ambermd.org
> Subject: [AMBER] Problem with mmpbsa
>
> Hi users,
>
> I have the following problem with the mmpbsa calculation:
>
> Loading and checking parameter files for compatibility...
> File "/opt/amber16/bin/MMPBSA.py", line 98, in <module>
> app.loadcheck_prmtops()
> File "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 572, in loadcheck_prmtops
> FILES.receptor_prmtop, FILES.ligand_prmtop)
> File
> "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
> line 109, in __init__
> self._validate()
> File
> "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
> line 876, in _validate
> raise PrmtopError('Complex natom != receptor natom + ligand natom')
> PrmtopError: Complex natom != receptor natom + ligand natom Exiting. All
> files have been retained.
>
> I already have tried to solve it but I couldn't.
>
> How can deal with this problem?
>
> Sincerely
>
> Tiffany
> Perfil p?blico*https://es.linkedin.com/in/tiffanirovira
> <https://es.linkedin.com/in/tiffanirovira>*
> [image: Ver imagen en tama?o completo]
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> ------------------------------
>
> Message: 6
> Date: Mon, 20 Feb 2017 04:46:38 -0800
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] Problem with mmpbsa
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <086ea8f5-eaa6-689d-2e28-8c9a2fc69208.cgl.ucsf.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> I'm guessing you are asked to specify 3 prmtop files, {complex,
> receptor, ligand}, and that they do not specify the appropriate sets of
> atoms. E.g. is your complex solvated?
>
> Bill
>
>
> On 2/20/17 4:11 AM, Tiffani Rovira wrote:
> > PrmtopError: Complex natom != receptor natom + ligand natom
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Mon, 20 Feb 2017 12:47:03 +0000
> From: Michael Shokhen <michael.shokhen.biu.ac.il>
> Subject: [AMBER] error in the input file
> To: "AMBER.ambermd.org" <AMBER.ambermd.org>
> Message-ID:
> <AM3PR04MB0565E71345E474E02AD2511DB65E0.AM3PR04MB0565.
> eurprd04.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Amber experts,
>
>
> Computer reports error in my input file for MD run.
>
> I need your help how to correct my input file.
>
> See details below.
>
>
> Thank you,
>
> Michael
>
>
> Input file: heat1.in
>
>
> protein restraint, heating 50K
>
> &cntrl
>
> imin=0,
>
> ntx=1,
>
> irest=0,
>
> ntc=2,
>
> ntf=2,
>
> tol=0.0000001,
>
> nstlim=50000,
>
> ntt=3,
>
> gamma_ln=1.0,
>
> ntr=1,
>
> ig=-1,
>
> ntpr=100,
>
> ntwr=10000,
>
> ntwx=100,
>
> dt=0.002,
>
> nmropt=1,
>
> ntb=1,
>
> ntp=0,
>
> cut=10.0,
>
> ioutfm=1,
>
> ntxo=2,
>
> /
>
> &wt
>
> type='TEMP0',
>
> istep1=0,
>
> istep2=50000,
>
> value1=0.0,
>
> value2=50.0
>
> &wt type='END' /
>
> Hold protein fixed
>
> 10.0
>
> RES 1 509
>
> /
>
> &rst
>
> restraint = "distance( (5716) (6163) )"
>
> restraint = "distance( (1297) (6163) )"
>
> restraint = "distance( (5756) (6163) )"
>
> restraint = "distance( (5348) (6163) )"
>
> restraint = "distance( (5134) (6163) )"
>
> restraint_wt = 50.0
>
> /
>
>
>
>
>
> Submitted job:
>
>
>
> nohup mpirun -np 2 $AMBERHOME/bin/pmemd.cuda.MPI -O -i heat1.in -o
> heat1.out -p ../*.prmtop -c ../2_/*.rst -x heat1.mdcrd -r heat1.rst -ref
> ../2_/*.rst &
>
>
>
> [1] 16844
>
> [enzyme03] 578 : namelist not terminated with / or &end
>
> Bad data for namelist object value2
>
> Cannot match namelist object name restraint
>
> namelist read: misplaced = sign
>
> Cannot match namelist object name "distance
>
> Cannot match namelist object name (
>
> Cannot match namelist object name (5716)
>
> Cannot match namelist object name (6163)
>
> Cannot match namelist object name )"
>
> Cannot match namelist object name restraint
>
> namelist read: misplaced = sign
>
> Cannot match namelist object name "distance
>
> Cannot match namelist object name (
>
> Cannot match namelist object name (1297)
>
> Cannot match namelist object name (6163)
>
> Cannot match namelist object name )"
>
> Cannot match namelist object name restraint
>
> namelist read: misplaced = sign
>
> Cannot match namelist object name "distance
>
> Cannot match namelist object name (
>
> Cannot match namelist object name (5756)
>
> Cannot match namelist object name (6163)
>
> Cannot match namelist object name )"
>
> Cannot match namelist object name restraint
>
> namelist read: misplaced = sign
>
> Cannot match namelist object name "distance
>
> Cannot match namelist object name (
>
> Cannot match namelist object name (5348)
>
> Cannot match namelist object name (6163)
>
> Cannot match namelist object name )"
>
> Cannot match namelist object name restraint
>
> namelist read: misplaced = sign
>
> Cannot match namelist object name "distance
>
> Cannot match namelist object name (
>
> Cannot match namelist object name (5134)
>
> Cannot match namelist object name (6163)
>
> Cannot match namelist object name )"
>
> Cannot match namelist object name restraint_wt
>
> namelist read: misplaced = sign
>
> Cannot match namelist object name 50.0
>
> --------------------------------------------------------------------------
>
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>
> with errorcode 1.
>
>
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>
> You may or may not see output from other processes, depending on
>
> exactly when Open MPI kills them.
>
> --------------------------------------------------------------------------
>
> --------------------------------------------------------------------------
>
> mpirun has exited due to process rank 0 with PID 16845 on
>
> node enzyme03 exiting without calling "finalize". This may
>
> have caused other processes in the application to be
>
> terminated by signals sent by mpirun (as reported here).
>
> --------------------------------------------------------------------------
>
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Mon, 20 Feb 2017 04:50:26 -0800
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] error in the input file
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <85ca7976-7e84-40a1-877a-7a6d15f892ca.cgl.ucsf.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Try not indenting the &rst block?
>
> Bill
>
>
> On 2/20/17 4:47 AM, Michael Shokhen wrote:
> > Dear Amber experts,
> >
> >
> > Computer reports error in my input file for MD run.
> >
> > I need your help how to correct my input file.
> >
> > See details below.
> >
> >
> > Thank you,
> >
> > Michael
> >
> >
> > Input file: heat1.in
> >
> >
> > protein restraint, heating 50K
> >
> > &cntrl
> >
> > imin=0,
> >
> > ntx=1,
> >
> > irest=0,
> >
> > ntc=2,
> >
> > ntf=2,
> >
> > tol=0.0000001,
> >
> > nstlim=50000,
> >
> > ntt=3,
> >
> > gamma_ln=1.0,
> >
> > ntr=1,
> >
> > ig=-1,
> >
> > ntpr=100,
> >
> > ntwr=10000,
> >
> > ntwx=100,
> >
> > dt=0.002,
> >
> > nmropt=1,
> >
> > ntb=1,
> >
> > ntp=0,
> >
> > cut=10.0,
> >
> > ioutfm=1,
> >
> > ntxo=2,
> >
> > /
> >
> > &wt
> >
> > type='TEMP0',
> >
> > istep1=0,
> >
> > istep2=50000,
> >
> > value1=0.0,
> >
> > value2=50.0
> >
> > &wt type='END' /
> >
> > Hold protein fixed
> >
> > 10.0
> >
> > RES 1 509
> >
> > /
> >
> > &rst
> >
> > restraint = "distance( (5716) (6163) )"
> >
> > restraint = "distance( (1297) (6163) )"
> >
> > restraint = "distance( (5756) (6163) )"
> >
> > restraint = "distance( (5348) (6163) )"
> >
> > restraint = "distance( (5134) (6163) )"
> >
> > restraint_wt = 50.0
> >
> > /
> >
> >
> >
> >
> >
> > Submitted job:
> >
> >
> >
> > nohup mpirun -np 2 $AMBERHOME/bin/pmemd.cuda.MPI -O -i heat1.in -o
> heat1.out -p ../*.prmtop -c ../2_/*.rst -x heat1.mdcrd -r heat1.rst -ref
> ../2_/*.rst &
> >
> >
> >
> > [1] 16844
> >
> > [enzyme03] 578 : namelist not terminated with / or &end
> >
> > Bad data for namelist object value2
> >
> > Cannot match namelist object name restraint
> >
> > namelist read: misplaced = sign
> >
> > Cannot match namelist object name "distance
> >
> > Cannot match namelist object name (
> >
> > Cannot match namelist object name (5716)
> >
> > Cannot match namelist object name (6163)
> >
> > Cannot match namelist object name )"
> >
> > Cannot match namelist object name restraint
> >
> > namelist read: misplaced = sign
> >
> > Cannot match namelist object name "distance
> >
> > Cannot match namelist object name (
> >
> > Cannot match namelist object name (1297)
> >
> > Cannot match namelist object name (6163)
> >
> > Cannot match namelist object name )"
> >
> > Cannot match namelist object name restraint
> >
> > namelist read: misplaced = sign
> >
> > Cannot match namelist object name "distance
> >
> > Cannot match namelist object name (
> >
> > Cannot match namelist object name (5756)
> >
> > Cannot match namelist object name (6163)
> >
> > Cannot match namelist object name )"
> >
> > Cannot match namelist object name restraint
> >
> > namelist read: misplaced = sign
> >
> > Cannot match namelist object name "distance
> >
> > Cannot match namelist object name (
> >
> > Cannot match namelist object name (5348)
> >
> > Cannot match namelist object name (6163)
> >
> > Cannot match namelist object name )"
> >
> > Cannot match namelist object name restraint
> >
> > namelist read: misplaced = sign
> >
> > Cannot match namelist object name "distance
> >
> > Cannot match namelist object name (
> >
> > Cannot match namelist object name (5134)
> >
> > Cannot match namelist object name (6163)
> >
> > Cannot match namelist object name )"
> >
> > Cannot match namelist object name restraint_wt
> >
> > namelist read: misplaced = sign
> >
> > Cannot match namelist object name 50.0
> >
> > ------------------------------------------------------------
> --------------
> >
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> >
> > with errorcode 1.
> >
> >
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> >
> > You may or may not see output from other processes, depending on
> >
> > exactly when Open MPI kills them.
> >
> > ------------------------------------------------------------
> --------------
> >
> > ------------------------------------------------------------
> --------------
> >
> > mpirun has exited due to process rank 0 with PID 16845 on
> >
> > node enzyme03 exiting without calling "finalize". This may
> >
> > have caused other processes in the application to be
> >
> > terminated by signals sent by mpirun (as reported here).
> >
> > ------------------------------------------------------------
> --------------
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 9
> Date: Mon, 20 Feb 2017 13:11:57 +0000
> From: Michael Shokhen <michael.shokhen.biu.ac.il>
> Subject: Re: [AMBER] error in the input file
> To: AMBER Mailing List <AMBER.ambermd.org>
> Message-ID:
> <AM3PR04MB056536F0B5677B54E7A27CCAB65E0.AM3PR04MB0565.
> eurprd04.prod.outlook.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Bill,
>
>
> Unfortunately, your suggestion does not work.
>
>
>
>
> Michael
> ________________________________
> From: Bill Ross <ross.cgl.ucsf.edu>
> Sent: Monday, February 20, 2017 2:50:26 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] error in the input file
>
> Try not indenting the &rst block?
>
> Bill
>
>
> On 2/20/17 4:47 AM, Michael Shokhen wrote:
> > Dear Amber experts,
> >
> >
> > Computer reports error in my input file for MD run.
> >
> > I need your help how to correct my input file.
> >
> > See details below.
> >
> >
> > Thank you,
> >
> > Michael
> >
> >
> > Input file: heat1.in
> >
> >
> > protein restraint, heating 50K
> >
> > &cntrl
> >
> > imin=0,
> >
> > ntx=1,
> >
> > irest=0,
> >
> > ntc=2,
> >
> > ntf=2,
> >
> > tol=0.0000001,
> >
> > nstlim=50000,
> >
> > ntt=3,
> >
> > gamma_ln=1.0,
> >
> > ntr=1,
> >
> > ig=-1,
> >
> > ntpr=100,
> >
> > ntwr=10000,
> >
> > ntwx=100,
> >
> > dt=0.002,
> >
> > nmropt=1,
> >
> > ntb=1,
> >
> > ntp=0,
> >
> > cut=10.0,
> >
> > ioutfm=1,
> >
> > ntxo=2,
> >
> > /
> >
> > &wt
> >
> > type='TEMP0',
> >
> > istep1=0,
> >
> > istep2=50000,
> >
> > value1=0.0,
> >
> > value2=50.0
> >
> > &wt type='END' /
> >
> > Hold protein fixed
> >
> > 10.0
> >
> > RES 1 509
> >
> > /
> >
> > &rst
> >
> > restraint = "distance( (5716) (6163) )"
> >
> > restraint = "distance( (1297) (6163) )"
> >
> > restraint = "distance( (5756) (6163) )"
> >
> > restraint = "distance( (5348) (6163) )"
> >
> > restraint = "distance( (5134) (6163) )"
> >
> > restraint_wt = 50.0
> >
> > /
> >
> >
> >
> >
> >
> > Submitted job:
> >
> >
> >
> > nohup mpirun -np 2 $AMBERHOME/bin/pmemd.cuda.MPI -O -i heat1.in -o
> heat1.out -p ../*.prmtop -c ../2_/*.rst -x heat1.mdcrd -r heat1.rst -ref
> ../2_/*.rst &
> >
> >
> >
> > [1] 16844
> >
> > [enzyme03] 578 : namelist not terminated with / or &end
> >
> > Bad data for namelist object value2
> >
> > Cannot match namelist object name restraint
> >
> > namelist read: misplaced = sign
> >
> > Cannot match namelist object name "distance
> >
> > Cannot match namelist object name (
> >
> > Cannot match namelist object name (5716)
> >
> > Cannot match namelist object name (6163)
> >
> > Cannot match namelist object name )"
> >
> > Cannot match namelist object name restraint
> >
> > namelist read: misplaced = sign
> >
> > Cannot match namelist object name "distance
> >
> > Cannot match namelist object name (
> >
> > Cannot match namelist object name (1297)
> >
> > Cannot match namelist object name (6163)
> >
> > Cannot match namelist object name )"
> >
> > Cannot match namelist object name restraint
> >
> > namelist read: misplaced = sign
> >
> > Cannot match namelist object name "distance
> >
> > Cannot match namelist object name (
> >
> > Cannot match namelist object name (5756)
> >
> > Cannot match namelist object name (6163)
> >
> > Cannot match namelist object name )"
> >
> > Cannot match namelist object name restraint
> >
> > namelist read: misplaced = sign
> >
> > Cannot match namelist object name "distance
> >
> > Cannot match namelist object name (
> >
> > Cannot match namelist object name (5348)
> >
> > Cannot match namelist object name (6163)
> >
> > Cannot match namelist object name )"
> >
> > Cannot match namelist object name restraint
> >
> > namelist read: misplaced = sign
> >
> > Cannot match namelist object name "distance
> >
> > Cannot match namelist object name (
> >
> > Cannot match namelist object name (5134)
> >
> > Cannot match namelist object name (6163)
> >
> > Cannot match namelist object name )"
> >
> > Cannot match namelist object name restraint_wt
> >
> > namelist read: misplaced = sign
> >
> > Cannot match namelist object name 50.0
> >
> > ------------------------------------------------------------
> --------------
> >
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> >
> > with errorcode 1.
> >
> >
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> >
> > You may or may not see output from other processes, depending on
> >
> > exactly when Open MPI kills them.
> >
> > ------------------------------------------------------------
> --------------
> >
> > ------------------------------------------------------------
> --------------
> >
> > mpirun has exited due to process rank 0 with PID 16845 on
> >
> > node enzyme03 exiting without calling "finalize". This may
> >
> > have caused other processes in the application to be
> >
> > terminated by signals sent by mpirun (as reported here).
> >
> > ------------------------------------------------------------
> --------------
> >
> >
> >
> > _______________________________________________
> > 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: 10
> Date: Mon, 20 Feb 2017 05:23:08 -0800
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] error in the input file
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <9d7a476f-8b42-a7bb-04ea-7b969ef38717.cgl.ucsf.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Does the group input end with a '/'? I thought that was just for
> namelist input.
>
> Bill
>
>
> On 2/20/17 5:11 AM, Michael Shokhen wrote:
> > RES 1 509
> >
> > /
>
>
>
>
> ------------------------------
>
> Message: 11
> Date: Mon, 20 Feb 2017 13:31:26 +0000
> From: Michael Shokhen <michael.shokhen.biu.ac.il>
> Subject: Re: [AMBER] error in the input file
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <AM3PR04MB0565AF6C8021D93E2CE85A04B65E0.AM3PR04MB0565.
> eurprd04.prod.outlook.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Bill,
>
>
> You can find all details in my email containing the input file and
> computer report you are asking about.
>
> I would appreciate if you would add corrections into my input file.
>
>
> Michael
>
>
>
>
> ________________________________
> From: Bill Ross <ross.cgl.ucsf.edu>
> Sent: Monday, February 20, 2017 3:23:08 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] error in the input file
>
> Does the group input end with a '/'? I thought that was just for
> namelist input.
>
> Bill
>
>
> On 2/20/17 5:11 AM, Michael Shokhen wrote:
> > RES 1 509
> >
> > /
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> ------------------------------
>
> Message: 12
> Date: Mon, 20 Feb 2017 05:36:25 -0800
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] error in the input file
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <d5e4d986-aba3-20e6-c292-bffee475bf4c.cgl.ucsf.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Sorry Michael,
>
> You will have to read in the manual how to end your group input
> properly. I think it's with 1 or 2 END lines, rather than '/' I quote
> from your input below.
>
> Bill
>
>
> On 2/20/17 5:31 AM, Michael Shokhen wrote:
> > Bill,
> >
> >
> > You can find all details in my email containing the input file and
> computer report you are asking about.
> >
> > I would appreciate if you would add corrections into my input file.
> >
> >
> > Michael
> >
> >
> >
> >
> > ________________________________
> > From: Bill Ross <ross.cgl.ucsf.edu>
> > Sent: Monday, February 20, 2017 3:23:08 PM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] error in the input file
> >
> > Does the group input end with a '/'? I thought that was just for
> > namelist input.
> >
> > Bill
> >
> >
> > On 2/20/17 5:11 AM, Michael Shokhen wrote:
> >> RES 1 509
> >>
> >> /
> >
> > _______________________________________________
> > 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: 13
> Date: Mon, 20 Feb 2017 13:47:09 +0000
> From: Michael Shokhen <michael.shokhen.biu.ac.il>
> Subject: Re: [AMBER] error in the input file
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <AM3PR04MB0565CF53F722C1A539A17D52B65E0.AM3PR04MB0565.
> eurprd04.prod.outlook.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Bill,
>
>
> Following your advise I have used two END lines.
>
> Unfortunately, it does not help.
>
>
> Michael
>
>
>
>
> ________________________________
> From: Bill Ross <ross.cgl.ucsf.edu>
> Sent: Monday, February 20, 2017 3:36:25 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] error in the input file
>
> Sorry Michael,
>
> You will have to read in the manual how to end your group input
> properly. I think it's with 1 or 2 END lines, rather than '/' I quote
> from your input below.
>
> Bill
>
>
> On 2/20/17 5:31 AM, Michael Shokhen wrote:
> > Bill,
> >
> >
> > You can find all details in my email containing the input file and
> computer report you are asking about.
> >
> > I would appreciate if you would add corrections into my input file.
> >
> >
> > Michael
> >
> >
> >
> >
> > ________________________________
> > From: Bill Ross <ross.cgl.ucsf.edu>
> > Sent: Monday, February 20, 2017 3:23:08 PM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] error in the input file
> >
> > Does the group input end with a '/'? I thought that was just for
> > namelist input.
> >
> > Bill
> >
> >
> > On 2/20/17 5:11 AM, Michael Shokhen wrote:
> >> RES 1 509
> >>
> >> /
> >
> > _______________________________________________
> > 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> ------------------------------
>
> Message: 14
> Date: Mon, 20 Feb 2017 14:51:16 +0100
> From: Qinghua Liao <scorpio.liao.gmail.com>
> Subject: Re: [AMBER] error in the input file
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <130a328f-53e2-c9b1-51ef-92e9d605b279.gmail.com>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Hello Michael,
>
> You can try with removing this "/" ?
>
> RES 1 509
>
> /
>
>
> All the best,
> Qinghua
>
> On 02/20/2017 02:47 PM, Michael Shokhen wrote:
> > Bill,
> >
> >
> > Following your advise I have used two END lines.
> >
> > Unfortunately, it does not help.
> >
> >
> > Michael
> >
> >
> >
> >
> > ________________________________
> > From: Bill Ross <ross.cgl.ucsf.edu>
> > Sent: Monday, February 20, 2017 3:36:25 PM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] error in the input file
> >
> > Sorry Michael,
> >
> > You will have to read in the manual how to end your group input
> > properly. I think it's with 1 or 2 END lines, rather than '/' I quote
> > from your input below.
> >
> > Bill
> >
> >
> > On 2/20/17 5:31 AM, Michael Shokhen wrote:
> >> Bill,
> >>
> >>
> >> You can find all details in my email containing the input file and
> computer report you are asking about.
> >>
> >> I would appreciate if you would add corrections into my input file.
> >>
> >>
> >> Michael
> >>
> >>
> >>
> >>
> >> ________________________________
> >> From: Bill Ross <ross.cgl.ucsf.edu>
> >> Sent: Monday, February 20, 2017 3:23:08 PM
> >> To: AMBER Mailing List
> >> Subject: Re: [AMBER] error in the input file
> >>
> >> Does the group input end with a '/'? I thought that was just for
> >> namelist input.
> >>
> >> Bill
> >>
> >>
> >> On 2/20/17 5:11 AM, Michael Shokhen wrote:
> >>> RES 1 509
> >>>
> >>> /
> >> _______________________________________________
> >> 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
> >
> > _______________________________________________
> > 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: 15
> Date: Mon, 20 Feb 2017 13:58:44 +0000
> From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
> Subject: Re: [AMBER] error in the input file
> To: <amber.ambermd.org>
> Message-ID: <20170220135844.058b7986.Hannes.Loeffler.stfc.ac.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> On Mon, 20 Feb 2017 12:47:03 +0000
> Michael Shokhen <michael.shokhen.biu.ac.il> wrote:
>
> > Dear Amber experts,
> >
> >
> > Computer reports error in my input file for MD run.
> >
> > I need your help how to correct my input file.
> >
> > See details below.
> >
> >
> > Thank you,
> >
> > Michael
> >
> >
> > Input file: heat1.in
> >
> >
> > protein restraint, heating 50K
> >
> > &cntrl
> >
> > imin=0,
> >
> > ntx=1,
> >
> > irest=0,
> >
> > ntc=2,
> >
> > ntf=2,
> >
> > tol=0.0000001,
> >
> > nstlim=50000,
> >
> > ntt=3,
> >
> > gamma_ln=1.0,
> >
> > ntr=1,
> >
> > ig=-1,
> >
> > ntpr=100,
> >
> > ntwr=10000,
> >
> > ntwx=100,
> >
> > dt=0.002,
> >
> > nmropt=1,
> >
> > ntb=1,
> >
> > ntp=0,
> >
> > cut=10.0,
> >
> > ioutfm=1,
> >
> > ntxo=2,
> >
> > /
> >
> > &wt
> >
> > type='TEMP0',
> >
> > istep1=0,
> >
> > istep2=50000,
> >
> > value1=0.0,
> >
> > value2=50.0
>
> This namelist is not terminated.
>
> >
> > &wt type='END' /
> >
> > Hold protein fixed
> >
> > 10.0
> >
> > RES 1 509
>
> This may have to go to the very end of the file and is not part of a
> namelist.
>
> > /
>
> There is no namelist that this slash would terminate. Namelists cannot
> be nested.
>
>
> > &rst
> >
> > restraint = "distance( (5716) (6163) )"
> >
> > restraint = "distance( (1297) (6163) )"
> >
> > restraint = "distance( (5756) (6163) )"
> >
> > restraint = "distance( (5348) (6163) )"
> >
> > restraint = "distance( (5134) (6163) )"
> >
> > restraint_wt = 50.0
> >
> > /
>
>
>
> ------------------------------
>
> Message: 16
> Date: Mon, 20 Feb 2017 14:38:08 +0000
> From: Michael Shokhen <michael.shokhen.biu.ac.il>
> Subject: Re: [AMBER] error in the input file
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <AM3PR04MB05653E64D85886820692BE1DB65E0.AM3PR04MB0565.
> eurprd04.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Many thanks for all of you who tried to help me.
>
> I have finally resolved the problem
>
> by "try-and-error" method, of course using some information from
>
> Amber manual.
>
> Please find below the correct variant of the input file.
>
> Hope the file could be useful for other amber users.
>
>
> All the best,
>
> Michael
>
>
> protein restraint, heating 50K
> &cntrl
> imin=0,
> ntx=1,
> irest=0,
> ntc=2,
> ntf=2,
> tol=0.0000001,
> nstlim=50000,
> ntt=3,
> gamma_ln=1.0,
> ntr=1,
> ig=-1,
> ntpr=100,
> ntwr=10000,
> ntwx=100,
> dt=0.002,
> nmropt=1,
> ntb=1,
> ntp=0,
> cut=10.0,
> ioutfm=1,
> ntxo=2,
> /
> &rst
> restraint = "distance( (5716) (6163) )"
> restraint = "distance( (1297) (6163) )"
> restraint = "distance( (5756) (6163) )"
> restraint = "distance( (5348) (6163) )"
> restraint = "distance( (5134) (6163) )"
> restraint_wt = 50.0
> /
> &wt
> type='TEMP0',
> istep1=0,
> istep2=50000,
> value1=0.0,
> value2=50.0 /
> &wt type='END' /
> Hold protein fixed
> 10.0
> RES 1 509
> END
> END
>
>
>
>
>
> ________________________________
> From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
> Sent: Monday, February 20, 2017 3:58 PM
> To: amber.ambermd.org
> Subject: Re: [AMBER] error in the input file
>
> On Mon, 20 Feb 2017 12:47:03 +0000
> Michael Shokhen <michael.shokhen.biu.ac.il> wrote:
>
> > Dear Amber experts,
> >
> >
> > Computer reports error in my input file for MD run.
> >
> > I need your help how to correct my input file.
> >
> > See details below.
> >
> >
> > Thank you,
> >
> > Michael
> >
> >
> > Input file: heat1.in
> >
> >
> > protein restraint, heating 50K
> >
> > &cntrl
> >
> > imin=0,
> >
> > ntx=1,
> >
> > irest=0,
> >
> > ntc=2,
> >
> > ntf=2,
> >
> > tol=0.0000001,
> >
> > nstlim=50000,
> >
> > ntt=3,
> >
> > gamma_ln=1.0,
> >
> > ntr=1,
> >
> > ig=-1,
> >
> > ntpr=100,
> >
> > ntwr=10000,
> >
> > ntwx=100,
> >
> > dt=0.002,
> >
> > nmropt=1,
> >
> > ntb=1,
> >
> > ntp=0,
> >
> > cut=10.0,
> >
> > ioutfm=1,
> >
> > ntxo=2,
> >
> > /
> >
> > &wt
> >
> > type='TEMP0',
> >
> > istep1=0,
> >
> > istep2=50000,
> >
> > value1=0.0,
> >
> > value2=50.0
>
> This namelist is not terminated.
>
> >
> > &wt type='END' /
> >
> > Hold protein fixed
> >
> > 10.0
> >
> > RES 1 509
>
> This may have to go to the very end of the file and is not part of a
> namelist.
>
> > /
>
> There is no namelist that this slash would terminate. Namelists cannot
> be nested.
>
>
> > &rst
> >
> > restraint = "distance( (5716) (6163) )"
> >
> > restraint = "distance( (1297) (6163) )"
> >
> > restraint = "distance( (5756) (6163) )"
> >
> > restraint = "distance( (5348) (6163) )"
> >
> > restraint = "distance( (5134) (6163) )"
> >
> > restraint_wt = 50.0
> >
> > /
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> ------------------------------
>
> Message: 17
> Date: Mon, 20 Feb 2017 10:14:48 -0500
> From: Thomas Pochapsky <pochapsk.brandeis.edu>
> Subject: [AMBER] changing chirality with ParmEd?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <7df7adb9-e315-f5f5-0b04-2e1b6c703c89.brandeis.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Is there a straighforward way to change the chirality of specific amino
> acid residues using parmed?
>
> Thanks,
> Tom Pochapsky
>
>
>
>
>
> ------------------------------
>
> Message: 18
> Date: Mon, 20 Feb 2017 10:33:18 -0500
> From: David Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Problem with mmpbsa
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20170220153318.zgl7fkcw4ga7b2nv.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Mon, Feb 20, 2017, Tiffani Rovira wrote:
> >
> > I have the following problem with the mmpbsa calculation:
> >
> > PrmtopError: Complex natom != receptor natom + ligand natom
> > Exiting. All files have been retained.
> >
> > I already have tried to solve it but I couldn't.
>
> I'm not sure that this can be easily debugged by email. Look at each of
> the
> three prtmop files (complex, receptor, ligand), and see if they contain the
> atoms you expect them to have. That will help narrow down the problem.
>
> ....good luck....dac
>
>
>
>
> ------------------------------
>
> Message: 19
> Date: Mon, 20 Feb 2017 09:55:56 -0600
> From: Brian Radak <brian.radak.accts.gmail.com>
> Subject: Re: [AMBER] Using CHARMM 36 force field in AMBER
> To: ?? <wumeng.shanghaitech.edu.cn>, AMBER Mailing List
> <amber.ambermd.org>
> Message-ID:
> <CANgqt_j4r62XAYZzXbHyzPbN6MHC9_GJ6w9u+CEndoqq+SV8Jg.mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> I strongly recommend copying additional emails like this to the listserv -
> archiving questions will help people with questions like this in the
> future.
>
> The most versatile and recent method for making force field modifications
> like this is the ParmEd program and library that is packaged with
> AmberTools. There is an updated CHAMBER equivalent therein:
>
> https://parmed.github.io/ParmEd/html/parmed.html#chamber
>
> I have not seen or done any specific tests to make sure that
> energies/forces are comparable between AMBER and other packages like CHARMM
> or NAMD when using files generated in this way.
>
> Ultimately, I expect the best way is to generate a CHARMM system in the
> usual way using something like CHARMM-GUI, although I'm not sure that this
> will automate the CHARMM36 inputs for AMBER (perhaps Jason or another
> ParmEd developer can comment on this?)
>
> HTH,
> Brian
>
> On Sat, Feb 18, 2017 at 9:32 PM, ?? <wumeng.shanghaitech.edu.cn> wrote:
>
> > Hi,
> >
> > Brian. You could see this e-mail because I searched on the Internet for
> > using CHARMM 36 force field in AMBER and I read your e-mail in AMBER
> > mailing list(http://archive.ambermd.org/201505/0427.html).
> >
> > I am worhing on a membrane protein sumulation in Amber, and I want to
> > apply CHARMM 36 force field to the membrane. I have searched some methods
> > such as using CHAMBER module in Amber, force switch in Amber16 and so on,
> > but I am still confused about how to do it. So could you share me your
> > experence on using CHARMM 36 force field in AMBER, more details is really
> > welcomed.
> >
> > I am looking forward to receiving your reply. Thank you in advance!
> >
> > All the best,
> > Wu Meng
> > Shanghai, China
> >
>
>
>
> --
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak.anl.gov
>
>
> ------------------------------
>
> Message: 20
> Date: Mon, 20 Feb 2017 18:36:18 +0000
> From: "Kasprzak, Wojciech (NIH/NCI) [C]" <kasprzaw.mail.nih.gov>
> Subject: Re: [AMBER] LeAP and FFs for Hybrid DNA/RNA structure
> To: "david.case.rutgers.edu" <david.case.rutgers.edu>, AMBER Mailing
> List <amber.ambermd.org>
> Message-ID: <D8142B0652A90D489D8B11566069E0E7413FB068.msgb03.nih.gov>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Dr. Case,
>
> Thank you for your answer about the FFs and DNA/RNA complexes. The bottom
> line is, I gather,
> that I should use both RNA and DNA parameters and that, in principle they
> can be employed with GB-neck2
> after proper PBradii are set.
>
> I apologize for my delayed response. I did not have full access to all the
> data over the weekend.
> I retested leap sessions in Amber 14 environment on two machines (separate
> campuses and administrators),
> and they both yielded identical PDB and PRMTOP output after leaprc.ff14SB
> & leaprc.ff14SB AND leaprc.parmbsc0_chiOL4_ezOL1
> were sourced (DNA chains have phosphate groups with P, O1P and O2P atom
> names and are capped by H5T & H3T, while
> RNA chains use PDB 3.x standard).
>
> One of our systems has Amber 16 installed and leap returns uniform atom
> names for DNA and RNA (P, OP1, OP2 and HO5'
> and HO3' respectively) after leaprc.RNA.OL3 and leaprc.DNA.OL15 are
> sourced. Unfortunately I ran into
> some criptic failure after the" addions mol Na+ 0" command and could not
> produce PRMTOP file for comparison with
> the previously created Amber 14 equivalent. (I will have to resolve this
> issue with our scientific apps administrators,
> since that was never a problem in the past.)
>
> If anybody can offer comments or warnings about RNA/DNA simulations, I
> will appreciate it very much.
>
> Best regards, Voytek Kasprzak
>
> Wojciech (Voytek) Kasprzak (Contractor)
> Analyst Programmer,
> Basic Science Program,
> Leidos Biomedical Research, Inc.
> Frederick National Laboratory for Cancer Research (FNLCR)
> Frederick, MD 21702
> (301) 846 5537
> http://binkley2.ncifcrf.gov/users/kasprzak
>
> ________________________________________
> From: David Case [david.case.rutgers.edu]
> Sent: Saturday, February 18, 2017 3:33 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] LeAP and FFs for Hybrid DNA/RNA structure
>
> On Fri, Feb 17, 2017, Kasprzak, Wojciech (NIH/NCI) [C] wrote:
> >
> > I am trying to run an Amber 14 MD simulation (explicit solvent, PME
> > and/or implicit solvent GB-neck2) of a hybrid nucleic acids structure
> > of 4 chains (2 DNA, 2 RNA) forming two DNA/RNA helices and one all-DNA
> > helix.
> >
> > I built two sets of parameter files (incl. water box and ions), one
> > based on leaprc.ff14SB ONLY (plus frcmod.ionsjc_tip3p) and the other
> > with leaprc.ff14SB AND leaprc.parmbsc0_chiOL4_ezOL1.
> >
> > I can immediately see that the DNA atoms in an output PDB files have
> > different names for the dual ff LEaP, and there are numerous differences
> > in the topology parameters files.
>
> Can you provide an example of the name differences? We re-worked the
> nomenclature for force fields in 2016 (for AmberTools16), and it's a little
> hard to go back to figure out how things used to be. I had thought that
> all our files had used IUPAC/PDB names for nucleic acids for some time.
>
> >
> > 1. Which is the correct (or better) way of preparing a DNA/RNA
> > simulation, and what is the meaning of a warning in the Amber 14 manual
> > (section 3.2.2) regarding the chi (chiOL4) modifications and shared
> > naming conventions for RNA and DNA.
>
> This, I think, has to do with atom *types*, not atom names; but atom types
> don't appear in PDB files.
>
> I'll leave it up to others to comment on any potential problems with
> DNA/RNA
> duplexes.
>
> >
> > 2. Can the same LEaP approach be applied to implicit solvent simulations
> > (GB-HCT igb=1 & mbondi and/or Gb-neck2 ibg=8 & mbondi3)?
>
> You need to either specify the PBRadii to be used at the time LEAP is run,
> or
> use ParmEd to change the radii after the fact. The igb choice is made at
> the
> time sander or parmed is run.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 21
> Date: Mon, 20 Feb 2017 14:42:18 -0500
> From: Hai Nguyen <nhai.qn.gmail.com>
> Subject: Re: [AMBER] changing chirality with ParmEd?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAFNMPM-OVLs1Dd35gsPL=-SeKmqQ7J1q0zTsROvr1EtOHDULGA.mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> AFAIN, there's not.
>
> Hai
>
> On Mon, Feb 20, 2017 at 10:14 AM, Thomas Pochapsky <pochapsk.brandeis.edu>
> wrote:
>
> > Is there a straighforward way to change the chirality of specific amino
> > acid residues using parmed?
> >
> > Thanks,
> > Tom Pochapsky
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 22
> Date: Mon, 20 Feb 2017 14:46:02 -0500
> From: Hai Nguyen <nhai.qn.gmail.com>
> Subject: Re: [AMBER] LeAP and FFs for Hybrid DNA/RNA structure
> To: AMBER Mailing List <amber.ambermd.org>
> Cc: "david.case.rutgers.edu" <david.case.rutgers.edu>
> Message-ID:
> <CAFNMPM_6sUnTTJu4wXOo66EzKABabWw4eQ5xU
> XACVBrNHheqhg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Mon, Feb 20, 2017 at 1:36 PM, Kasprzak, Wojciech (NIH/NCI) [C] <
> kasprzaw.mail.nih.gov> wrote:
>
> > Dear Dr. Case,
> >
> > Thank you for your answer about the FFs and DNA/RNA complexes. The
> bottom
> > line is, I gather,
> > that I should use both RNA and DNA parameters and that, in principle they
> > can be employed with GB-neck2
> > after proper PBradii are set.
> >
> > I apologize for my delayed response. I did not have full access to all
> the
> > data over the weekend.
> > I retested leap sessions in Amber 14 environment on two machines
> (separate
> > campuses and administrators),
> > and they both yielded identical PDB and PRMTOP output after
> leaprc.ff14SB
> > & leaprc.ff14SB AND leaprc.parmbsc0_chiOL4_ezOL1
> > were sourced (DNA chains have phosphate groups with P, O1P and O2P atom
> > names and are capped by H5T & H3T, while
> > RNA chains use PDB 3.x standard).
> >
> > One of our systems has Amber 16 installed and leap returns uniform atom
> > names for DNA and RNA (P, OP1, OP2 and HO5'
> > and HO3' respectively) after leaprc.RNA.OL3 and leaprc.DNA.OL15 are
> > sourced.
>
>
>
>
> > Unfortunately I ran into
> > some criptic failure after the" addions mol Na+ 0" command
>
>
> hi, what is the failure?
>
>
> > and could not produce PRMTOP file for comparison with
> > the previously created Amber 14 equivalent.
>
>
> PRMTOP files between two versions are expected to be different. You should
> check the energies.
>
> (Dan Roe said a bit in topic:
> [AMBER] Differences using leaprc.ff14SB from AmberTools15 and
> oldff/leaprc.ff14SB from AmberTools16)
>
> Hai
>
>
>
> > (I will have to resolve this issue with our scientific apps
> administrators,
> > since that was never a problem in the past.)
> >
> > If anybody can offer comments or warnings about RNA/DNA simulations, I
> > will appreciate it very much.
> >
> > Best regards, Voytek Kasprzak
> >
> > Wojciech (Voytek) Kasprzak (Contractor)
> > Analyst Programmer,
> > Basic Science Program,
> > Leidos Biomedical Research, Inc.
> > Frederick National Laboratory for Cancer Research (FNLCR)
> > Frederick, MD 21702
> > (301) 846 5537
> > http://binkley2.ncifcrf.gov/users/kasprzak
> >
> > ________________________________________
> > From: David Case [david.case.rutgers.edu]
> > Sent: Saturday, February 18, 2017 3:33 PM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] LeAP and FFs for Hybrid DNA/RNA structure
> >
> > On Fri, Feb 17, 2017, Kasprzak, Wojciech (NIH/NCI) [C] wrote:
> > >
> > > I am trying to run an Amber 14 MD simulation (explicit solvent, PME
> > > and/or implicit solvent GB-neck2) of a hybrid nucleic acids structure
> > > of 4 chains (2 DNA, 2 RNA) forming two DNA/RNA helices and one all-DNA
> > > helix.
> > >
> > > I built two sets of parameter files (incl. water box and ions), one
> > > based on leaprc.ff14SB ONLY (plus frcmod.ionsjc_tip3p) and the other
> > > with leaprc.ff14SB AND leaprc.parmbsc0_chiOL4_ezOL1.
> > >
> > > I can immediately see that the DNA atoms in an output PDB files have
> > > different names for the dual ff LEaP, and there are numerous
> differences
> > > in the topology parameters files.
> >
> > Can you provide an example of the name differences? We re-worked the
> > nomenclature for force fields in 2016 (for AmberTools16), and it's a
> little
> > hard to go back to figure out how things used to be. I had thought that
> > all our files had used IUPAC/PDB names for nucleic acids for some time.
> >
> > >
> > > 1. Which is the correct (or better) way of preparing a DNA/RNA
> > > simulation, and what is the meaning of a warning in the Amber 14 manual
> > > (section 3.2.2) regarding the chi (chiOL4) modifications and shared
> > > naming conventions for RNA and DNA.
> >
> > This, I think, has to do with atom *types*, not atom names; but atom
> types
> > don't appear in PDB files.
> >
> > I'll leave it up to others to comment on any potential problems with
> > DNA/RNA
> > duplexes.
> >
> > >
> > > 2. Can the same LEaP approach be applied to implicit solvent
> simulations
> > > (GB-HCT igb=1 & mbondi and/or Gb-neck2 ibg=8 & mbondi3)?
> >
> > You need to either specify the PBRadii to be used at the time LEAP is
> run,
> > or
> > use ParmEd to change the radii after the fact. The igb choice is made at
> > the
> > time sander or parmed is run.
> >
> > ....dac
> >
> >
> > _______________________________________________
> > 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
> >
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 1852, Issue 1
> **************************************
>
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Received on Tue Feb 21 2017 - 03:00:02 PST
