dear sir,
If i use small cut value such as 6 Ang., Would the periodic boundary
condition maintained or not. Because in a AMBER tutorial i have
studied that the lower cut off may destroy the PBC.
So please guide me in this regard.
On 11/22/14, amber-request.ambermd.org <amber-request.ambermd.org> wrote:
> Send AMBER mailing list submissions to
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>
> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Can you use cholesterol lipid 11 parameters and lipid 14
> lipid parameters? (Jonathan Gough)
> 2. Re: Errors compiling Amber 14 after applying update 7
> (Jason Swails)
> 3. Re: PBSA error (Jason Swails)
> 4. Re: PBSA error (David A Case)
> 5. Re: Errors compiling Amber 14 after applying update 7
> (David A Case)
> 6. Re: Errors compiling Amber 14 after applying update 7
> (Ross Walker)
> 7. Re: PBSA error (David A Case)
> 8. Re: PBSA error (Kshatresh Dutta Dubey)
> 9. Re: PBSA error (Kshatresh Dutta Dubey)
> 10. Re: PBSA error (Ray Luo, Ph.D.)
> 11. MMPBSA.py bug with amber mask for stability/QH calculations
> (Lawrenz, Morgan)
> 12. Re: MMPBSA.py bug with amber mask for stability/QH
> calculations (Jason Swails)
> 13. The error when install amber12+AmberTools13 on Ubuntucd (Biao Ma)
> 14. Re: The error when install amber12+AmberTools13 on Ubuntucd
> (Jason Swails)
> 15. cut value in minimisation (Robin Jain)
> 16. Bug Report (Liu, Hui)
> 17. Re: cut value in minimisation (Jason Swails)
> 18. Re: Bug Report (Jason Swails)
> 19. cyclic peptide side chains (Maria Diaz)
> 20. about nab (m13654940810)
> 21. Re: cut value in minimisation (David A Case)
> 22. Re: cyclic peptide side chains (David A Case)
> 23. Re: about nab (David A Case)
> 24. Re: Help generating Heme parameters (Pengfei Li)
> 25. Issues with Cholesterol lipid11, lipid14 and lipid14_supp.lib
> (Jonathan Gough)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 20 Nov 2014 15:06:19 -0500
> From: Jonathan Gough <jonathan.d.gough.gmail.com>
> Subject: [AMBER] Can you use cholesterol lipid 11 parameters and lipid
> 14 lipid parameters?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAFkCv1S9jjn-+bhCyvE73f=3rRr-X-uK3-eD9LiL+DDkNmynWA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi All,
>
> I was wondering, can you use the cholesterol parameters from lipid 11
> alongside the lipid 14 parameters? (I am assuming there still aren't
> any lipid 14 cholesterol parameters)
>
> If so (and it's not ill advised), is there something specific I need
> to do in leap to make sure lipid 14 parameters are used for the lipid?
>
> If it is better to generate parameters (non GAFF) for cholesterol, can
> someone comment on the what level of QM aught to be used (via
> Paramfit) to best match the lipid 14 parameter set?
>
> Thanks,
> Jonathan
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 20 Nov 2014 15:17:51 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Errors compiling Amber 14 after applying update 7
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3pqqD4E9=auGVZPRu6gw5rnvyLySgsZi_twxMsAY-p82A.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Thu, Nov 20, 2014 at 12:45 PM, Bob Healey <healer.rpi.edu> wrote:
>
>> Just got my Amber license this week, unpacked everything and started
>> compiling according to the manual. The first pass through (./configure
>> gnu && make install) applied up to update 6. When I went to do the MPI
>> build, the update script found update 7. After applying it, I can not
>> get the compilation to complete. I even deleted my source tree and
>> started over a few times. Before I roll back to update 6, I was
>> wondering if anyone on this list had any advice for me. I am using
>> Fedora 19, with stock compilers.
>>
>> Thank you.
>>
>> gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native
>> -I/usr/local/amber/amber14/include -c shake.F90
>> shake.F90:940.132:
>>
>> tected in equilibrium bond length for',/5x,'SHAKEn TI
>> atoms',1x,i8,2x,i8,2x
>> 1
>> Error: Unexpected end of format string in format string at (1)
>> shake.F90:941.132:
>>
>> nchronized from V0. ',/1x,'Consider using noshake mask or disabling
>> SHAKE.'
>> 1
>> Error: Unexpected end of format string in format string at (1)
>> shake.F90:932.41:
>>
>
> ?I just tried this update myself and got the same error. The GNU compilers
> have a much shorter line length limit than the Intel compilers. What this
> means is that this update was not tested with the GNU compilers before it
> was released, so another update will be required to fix that.
>
> For the time being, you can use update_amber to revert to Amber/6 like so:
>
> cd $AMBERHOME
> ./update_amber --revert-to Amber/6
>
> Then recompile (making sure to say *no* to updates when asked).
>
> ?Hope this helps, and thanks for the report,
> Jason?
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 20 Nov 2014 15:21:23 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] PBSA error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3rt+ffKr+UEXmB8JxOMG6weYXGyJ4TSN55cF10A_VhLbw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Thu, Nov 20, 2014 at 1:10 PM, Kshatresh Dutta Dubey
> <kshatresh.gmail.com>
> wrote:
>
>> Dear Users,
>>
>> I am using amber 14 for pbsa program. When I am trying to run the pbsa
>> with
>> :
>> pbsa -O -i pbsa.in -o pbsa.out -p ../dimer-sb-wat.prmtop -c
>> dimer-SB-run1.rst &
>>
>> It is showing error:
>> Program received signal SIGSEGV: Segmentation fault - invalid memory
>> reference.
>>
>> Backtrace for this error:
>> #0 0x2B776A0A34C7
>> #1 0x2B776A0A3B0E
>> #2 0x2B776AB3463F
>> #3 0x2B776A169990
>> #4 0x2B776A16A4A8
>> #5 0x2B776A16E2DC
>> #6 0x4C3139 in rdparm2_
>> #7 0x40574F in pbsa_
>> ......
>> segmentation fault. I am using netcdf format of rst file, while my input
>>
>
> ?Try using an ASCII format coordinate file. I don't know that PBSA
> supports NetCDF restart files.
> ?
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 20 Nov 2014 15:32:45 -0500
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] PBSA error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20141120203245.GB8738.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Thu, Nov 20, 2014, Kshatresh Dutta Dubey wrote:
>>
>> I am using amber 14 for pbsa program. When I am trying to run the pbsa
>> with
>> :
>> pbsa -O -i pbsa.in -o pbsa.out -p ../dimer-sb-wat.prmtop -c
>> dimer-SB-run1.rst &
>>
>> It is showing error:
>> Program received signal SIGSEGV: Segmentation fault - invalid memory
>> reference.
>
>> segmentation fault. I am using netcdf format of rst file...
>
> Try converting the rst file to the older (formatted) format: in cpptraj
>
> trajin dimer-SB-run1.rst
> trajin dimer-SB-run1.rst7 restart
>
> I'm guessing that pbsa doesn't know how to read the netcdf restart format.
>
> Let us know if that doesn't work....good luck....dac
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 20 Nov 2014 15:33:32 -0500
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] Errors compiling Amber 14 after applying update 7
> To: AMBER Mailing List <amber.ambermd.org>
> Cc: joekaus.gmail.com, Ross Walker <rcw.sdsc.edu>
> Message-ID: <20141120203332.GC8738.biomaps.rutgers.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> On Thu, Nov 20, 2014, Bob Healey wrote:
>
>> Just got my Amber license this week, unpacked everything and started
>> compiling according to the manual. The first pass through (./configure
>> gnu && make install) applied up to update 6. When I went to do the MPI
>> build, the update script found update 7. After applying it, I can not
>> get the compilation to complete.
>
> Aargh...update 7 to pmemd, which was just posted this week, is broken,
> and you are the lucky first person to encounter it.
>
> Joe used lines longer that 132 characters, which will choke many compilers.
>
> A patch file is attached, or just make the changes in formats 1111 and
> 1112 by hand. We'll post an updated patch as soon as possible (cc-ing to
> Joe
> and Ross...please make sure that this is the only issue.)
>
> Thanks for the report.....dac
>
> -------------- next part --------------
> diff --git a/src/pmemd/src/shake.F90 b/src/pmemd/src/shake.F90
> index 33d9f4b..fb11798 100644
> --- a/src/pmemd/src/shake.F90
> +++ b/src/pmemd/src/shake.F90
> .. -937,8 +937,11 .. subroutine nonfastwat_shake_setup
> if (master .and. write_msg) write(mdout, 1112)
> end if
>
> - 1111 format(1x,'WARNING: Large deviation of ',f4.3,' detected in
> equilibrium bond length for',/5x,'SHAKEn TI atoms',1x,i8,2x,i8,2x,' and
> ',i8,2x,i8)
> - 1112 format(1x,'Coordinates for common atoms will be synchronized from
> V0. ',/1x,'Consider using noshake mask or disabling SHAKE.',/)
> + 1111 format(1x,'WARNING: Large deviation of ',f4.3, &
> + ' detected in equilibrium bond length for',/5x,'SHAKEn TI atoms', &
> + 1x,i8,2x,i8,2x,' and ',i8,2x,i8)
> + 1112 format(1x,'Coordinates for common atoms will be synchronized from
> V0. ',&
> + /1x,'Consider using noshake mask or disabling SHAKE.',/)
> 1113 format(1x,'WARNING: SHAKEn bond for atoms ', i8,1x,i8, ' is
> partially softcore.')
> return
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 20 Nov 2014 12:38:46 -0800
> From: Ross Walker <ross.rosswalker.co.uk>
> Subject: Re: [AMBER] Errors compiling Amber 14 after applying update 7
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <D093913F.4CEF2%ross.rosswalker.co.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> Joe has already prepared a fix - it will be posted shortly once one of us
> has decent internet access.
>
>
>
>
> On 11/20/14, 12:33 PM, "David A Case" <case.biomaps.rutgers.edu> wrote:
>
>>On Thu, Nov 20, 2014, Bob Healey wrote:
>>
>>> Just got my Amber license this week, unpacked everything and started
>>> compiling according to the manual. The first pass through (./configure
>>> gnu && make install) applied up to update 6. When I went to do the MPI
>>> build, the update script found update 7. After applying it, I can not
>>> get the compilation to complete.
>>
>>Aargh...update 7 to pmemd, which was just posted this week, is broken,
>>and you are the lucky first person to encounter it.
>>
>>Joe used lines longer that 132 characters, which will choke many
>>compilers.
>>
>>A patch file is attached, or just make the changes in formats 1111 and
>>1112 by hand. We'll post an updated patch as soon as possible (cc-ing to
>>Joe
>>and Ross...please make sure that this is the only issue.)
>>
>>Thanks for the report.....dac
>>
>>_______________________________________________
>>AMBER mailing list
>>AMBER.ambermd.org
>>http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 20 Nov 2014 15:42:25 -0500
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] PBSA error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20141120204225.GA17023.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
>> On Thu, Nov 20, 2014, Kshatresh Dutta Dubey wrote:
>> >
>> > I am using amber 14 for pbsa program. When I am trying to run the pbsa
>> > with
>> > :
>> > pbsa -O -i pbsa.in -o pbsa.out -p ../dimer-sb-wat.prmtop -c
>> > dimer-SB-run1.rst &
>> >
>> > It is showing error:
>> > Program received signal SIGSEGV: Segmentation fault - invalid memory
>> > reference.
>>
>> > segmentation fault. I am using netcdf format of rst file...
>>
>> Try converting the rst file to the older (formatted) format: in cpptraj
>>
>> trajin dimer-SB-run1.rst
>> trajin dimer-SB-run1.rst7 restart
> ^^^^^^^ <= trajout here, not trajin.....
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Thu, 20 Nov 2014 22:45:49 +0200
> From: Kshatresh Dutta Dubey <kshatresh.gmail.com>
> Subject: Re: [AMBER] PBSA error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAF3NQ5cZK+OuuPbcDftDVTfc_qaakP-Qx8h_X6KOaXKgOpGa5A.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Thanks David and Jason for your suggestions.
>
> Regards
> Kshatresh
>
> On Thu, Nov 20, 2014 at 10:42 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
>> > On Thu, Nov 20, 2014, Kshatresh Dutta Dubey wrote:
>> > >
>> > > I am using amber 14 for pbsa program. When I am trying to run the
>> > > pbsa
>> with
>> > > :
>> > > pbsa -O -i pbsa.in -o pbsa.out -p ../dimer-sb-wat.prmtop -c
>> > > dimer-SB-run1.rst &
>> > >
>> > > It is showing error:
>> > > Program received signal SIGSEGV: Segmentation fault - invalid memory
>> > > reference.
>> >
>> > > segmentation fault. I am using netcdf format of rst file...
>> >
>> > Try converting the rst file to the older (formatted) format: in cpptraj
>> >
>> > trajin dimer-SB-run1.rst
>> > trajin dimer-SB-run1.rst7 restart
>> ^^^^^^^ <= trajout here, not trajin.....
>>
>> ...dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> ------------------------------
>
> Message: 9
> Date: Thu, 20 Nov 2014 22:52:22 +0200
> From: Kshatresh Dutta Dubey <kshatresh.gmail.com>
> Subject: Re: [AMBER] PBSA error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAF3NQ5csXJxScEvFJDhMx0GbR4RnU1bJ6bK4PK-Upqn2X2Oaog.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Jason and David,
>
> I re-ran the pbsa using old styled inpcrd, but unfortunately I am getting
> same error.
>
> Regards
> Kshatresh
>
> On Thu, Nov 20, 2014 at 10:45 PM, Kshatresh Dutta Dubey
> <kshatresh.gmail.com
>> wrote:
>
>> Thanks David and Jason for your suggestions.
>>
>> Regards
>> Kshatresh
>>
>> On Thu, Nov 20, 2014 at 10:42 PM, David A Case <case.biomaps.rutgers.edu>
>> wrote:
>>
>>> > On Thu, Nov 20, 2014, Kshatresh Dutta Dubey wrote:
>>> > >
>>> > > I am using amber 14 for pbsa program. When I am trying to run the
>>> pbsa with
>>> > > :
>>> > > pbsa -O -i pbsa.in -o pbsa.out -p ../dimer-sb-wat.prmtop -c
>>> > > dimer-SB-run1.rst &
>>> > >
>>> > > It is showing error:
>>> > > Program received signal SIGSEGV: Segmentation fault - invalid memory
>>> > > reference.
>>> >
>>> > > segmentation fault. I am using netcdf format of rst file...
>>> >
>>> > Try converting the rst file to the older (formatted) format: in
>>> > cpptraj
>>> >
>>> > trajin dimer-SB-run1.rst
>>> > trajin dimer-SB-run1.rst7 restart
>>> ^^^^^^^ <= trajout here, not trajin.....
>>>
>>> ...dac
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>>
>>
>>
>
>
> --
> With best regards
> ************************************************************************************************
> Kshatresh Dutta Dubey
> Post Doctoral Researcher,
> Lise Meitner Center for Computational Quantum Chemistry
> Hebrew University of Jerusalem Israel
> Jerusalem, Israel
>
>
> ------------------------------
>
> Message: 10
> Date: Thu, 20 Nov 2014 14:49:07 -0800
> From: "Ray Luo, Ph.D." <ray.luo.uci.edu>
> Subject: Re: [AMBER] PBSA error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CALRp-wo0VUCL4QqzFZX-QWBa5jA3Mqn3dGzkEKGc4LOXEJxr7A.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Interesting ? please email me your files (inpcrd type with prmtop
> file) off the list so I can take a look ?
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor,
> Biochemistry, Molecular Biophysics, Chemical Physics,
> Chemical and Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
>
> On Thu, Nov 20, 2014 at 12:52 PM, Kshatresh Dutta Dubey
> <kshatresh.gmail.com> wrote:
>> Hi Jason and David,
>>
>> I re-ran the pbsa using old styled inpcrd, but unfortunately I am getting
>> same error.
>>
>> Regards
>> Kshatresh
>>
>> On Thu, Nov 20, 2014 at 10:45 PM, Kshatresh Dutta Dubey
>> <kshatresh.gmail.com
>>> wrote:
>>
>>> Thanks David and Jason for your suggestions.
>>>
>>> Regards
>>> Kshatresh
>>>
>>> On Thu, Nov 20, 2014 at 10:42 PM, David A Case
>>> <case.biomaps.rutgers.edu>
>>> wrote:
>>>
>>>> > On Thu, Nov 20, 2014, Kshatresh Dutta Dubey wrote:
>>>> > >
>>>> > > I am using amber 14 for pbsa program. When I am trying to run the
>>>> pbsa with
>>>> > > :
>>>> > > pbsa -O -i pbsa.in -o pbsa.out -p ../dimer-sb-wat.prmtop -c
>>>> > > dimer-SB-run1.rst &
>>>> > >
>>>> > > It is showing error:
>>>> > > Program received signal SIGSEGV: Segmentation fault - invalid
>>>> > > memory
>>>> > > reference.
>>>> >
>>>> > > segmentation fault. I am using netcdf format of rst file...
>>>> >
>>>> > Try converting the rst file to the older (formatted) format: in
>>>> > cpptraj
>>>> >
>>>> > trajin dimer-SB-run1.rst
>>>> > trajin dimer-SB-run1.rst7 restart
>>>> ^^^^^^^ <= trajout here, not trajin.....
>>>>
>>>> ...dac
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>> --
>> With best regards
>> ************************************************************************************************
>> Kshatresh Dutta Dubey
>> Post Doctoral Researcher,
>> Lise Meitner Center for Computational Quantum Chemistry
>> Hebrew University of Jerusalem Israel
>> Jerusalem, Israel
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 11
> Date: Thu, 20 Nov 2014 23:34:06 +0000
> From: "Lawrenz, Morgan" <mlawrenz.amgen.com>
> Subject: [AMBER] MMPBSA.py bug with amber mask for stability/QH
> calculations
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <EFCFA7E4268F9D45A6B9049C0E7653418B08D1.usso-pmsg-mbx01.am.corp.amgen.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi all,
> I've found a bug in MMPBSA.py, in the amber mask output when running QH
> entropy calculations, specifically when a "stability" calculation is
> performed, i.e. when computing quantities for a single species instead of a
> complex.
> I found that the Mask() method of the MMPBSA_System class in parm_setup.py
> is printing incorrect amber masks, starting from zero and without the colon
> (:). I was getting masks in the resulting ptraj scripts like this for a 3
> residue peptide:
> matrix mwcovar name comp.matrix ,0-3
>
> The bug is actually in the method _stability_mask(), the loops and
> incrementing is off. I put in my own easy fixes but thought I'd bring it to
> your attention.
> Thanks!
> Morgan
>
>
> ------------------------------
>
> Message: 12
> Date: Thu, 20 Nov 2014 18:47:42 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] MMPBSA.py bug with amber mask for stability/QH
> calculations
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <5CAC323F-ACC7-4690-9D19-172A52A90275.gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
>
>> On Nov 20, 2014, at 6:34 PM, Lawrenz, Morgan <mlawrenz.amgen.com> wrote:
>>
>> Hi all,
>> I've found a bug in MMPBSA.py, in the amber mask output when running QH
>> entropy calculations, specifically when a "stability" calculation is
>> performed, i.e. when computing quantities for a single species instead of
>> a complex.
>> I found that the Mask() method of the MMPBSA_System class in parm_setup.py
>> is printing incorrect amber masks, starting from zero and without the
>> colon (:). I was getting masks in the resulting ptraj scripts like this
>> for a 3 residue peptide:
>> matrix mwcovar name comp.matrix ,0-3
>>
>> The bug is actually in the method _stability_mask(), the loops and
>> incrementing is off. I put in my own easy fixes but thought I'd bring it
>> to your attention.
>
> Thanks for finding this! Do you happen to have your fix handy so I can add
> it to the main code?
>
> Thanks!
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
>
> ------------------------------
>
> Message: 13
> Date: Fri, 21 Nov 2014 11:31:18 +0900
> From: Biao Ma <jackyma1981.gmail.com>
> Subject: [AMBER] The error when install amber12+AmberTools13 on
> Ubuntucd
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAzfqsQ+7DP7CmXiVqpd3QJd1N8fqECuS9FKw2RU1WJq=N6d7g.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi, amber users.
>
> When I install the amber12 on my Ubuntu pc, I got the error messge when I
> do 'make install'.
> what I did is :
>
> #####################
> # First time I did
> #####################
>
> 1.
>
> sudo apt-get update
> 2.
>
> sudo apt-get install csh flex patch gfortran g++ make xorg-dev
> libbz2-dev
> 3.
>
> sudo apt-get install python-tk python-dev python-matplotlib python-numpy
> python-scipy
> 4.
>
> sudo apt-get install openmpi-bin libopenmpi-dev
> 5.
>
> cd $AMBERHOME && make clean (the source files is copyed from another
> Linux PC, which was successed installed amber by ./configure -mpi -rism
> intel, make install)
> 6.
>
> ./configure gnu
> 7. make install (Error is out)
>
>
>
> the last part of stdout message after 'make install':
>
> cd ../lib && make nxtsec.o random.o
> make[3]: Entering directory `/home/mabiao/bin/amber12/AmberTools/src/lib'
> make[3]: `nxtsec.o' is up to date.
> make[3]: `random.o' is up to date.
> make[3]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src/lib'
> cd ../lapack && make install
> make[3]: Entering directory
> `/home/mabiao/bin/amber12/AmberTools/src/lapack'
> make[3]: Nothing to be done for `install'.
> make[3]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src/lapack'
> cd ../blas && make install
> make[3]: Entering directory `/home/mabiao/bin/amber12/AmberTools/src/blas'
> make[3]: Nothing to be done for `install'.
> make[3]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src/blas'
> cd ../arpack && make install
> make[3]: Entering directory
> `/home/mabiao/bin/amber12/AmberTools/src/arpack'
> make[3]: Nothing to be done for `install'.
> make[3]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src/arpack'
> gfortran -DFFTW -DBINTRAJ -ffree-form
> -I/home/mabiao/bin/amber12/include -I/home/mabiao/bin/amber12/include
> -o pbsa dsvdc.o pbsa.o pb_read.o pb_write.o getcoor.o runmd.o runmin.o
> force.o pb_init.o sa_driver.o np_force.o pb_force.o pb_fddrv.o pb_iimdrv.o
> pb_nlsolver.o pb_exmol.o pb_mpfrc.o pb_direct.o pb_list.o timer.o
> pb_fftsolv.o pb_fft.o egb.o ene.o locmem.o myopen.o rdparm.o pb_lsolver.o
> decomp.o rgroup.o rfree.o debug.o coed20.o indexg.o irre32.o phidev.o
> project.o qld.o coed6.o irre31.o miniop.o iimod.o prodis.o qint.o
> wint.o transf.o curv.o GrToPr.o jumps.o problem.o IIM.o regular.o gmres.o
> daxpy.o ddot.o dheqr.o dpigmr.o dscal.o dslui2.o dxlcal.o dchkw.o
> dgmres.o dnrm2.o drlcal.o dsilus.o dslui.o isdgmr.o dcopy.o dhels.o
> dorth.o ds2y.o dslugm.o dsmv.o qs2i1d.o d1mach.o fdump.o
> i1mach.o j4save.o xercnt.o xerhlt.o xermsg.o xerprn.o xersve.o
> xgetua.o bicg.o dbcg.o dslui4.o dsluti.o dsmtv.o dslubc.o isdbcg.o
> pb_chkfrc.o svdcmp.o svbksb.o pythag.o pb_augdrv.o gmresX.o interpX.o
> matvec3.o gen_dx_file.o aug_iccg.o membrane.o fftw3.o \
> ../lib/nxtsec.o ../lib/random.o -lfftw3 \
> -L/home/mabiao/bin/amber12/lib -larpack -llapack -lblas
> /usr/bin/ld: skipping incompatible /home/mabiao/bin/amber12/lib/libfftw3.a
> when searching for -lfftw3
> /usr/bin/ld: cannot find -lfftw3
> collect2: error: ld returned 1 exit status
> make[2]: *** [pbsa] Error 1
> make[2]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src/pbsa'
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src'
> make: *** [install] Error 2
>
> when I check the folder ~/amber12/lib/ I found some older files was created
> at 2013,
> -rw-r--r-- 1 mabiao mabiao 3.0M Nov 28 2013 libfftw3.a
> -rw-r--r-- 1 mabiao mabiao 80K Nov 28 2013 libxblas-amb.a
> -rw-r--r-- 1 mabiao mabiao 1.2M Nov 28 2013 libnab.a
> -rw-r--r-- 1 mabiao mabiao 1.6M Nov 28 2013 libnetcdf.a
> -rwxr-xr-x 1 mabiao mabiao 898 Nov 20 15:02 libDiagnostics.la
> -rw-r--r-- 1 mabiao mabiao 5.8K Nov 20 15:02 libDiagnostics.a
> -rwxr-xr-x 1 mabiao mabiao 886 Nov 20 15:02 libtinyxml.la
> -rw-r--r-- 1 mabiao mabiao 120K Nov 20 15:02 libtinyxml.a
>
> why the old file not removed when 'make clean'?
>
> #####################
> # second time I did
> #####################
>
> I try to delete all the files in $AMBERHOME/lib/, and then do
> make clean
> ./configure gnu
> make install
>
> this time I got the another error message
>
> gcc: error: /home/mabiao/bin/amber12/lib/libnetcdf.a: No such file or
> directory
> make[2]: *** [rdparm] Error 1
> make[2]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src/ptraj'
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src'
> make: *** [install] Error 2
>
> I check the $AMBERHOME/lib/ folder and found there no libnetcdf.a ,
>
> The files in $AMBERHOME/lib/ folder how to be generated ?
> Who can give me some advice ?
>
> Thanks a lot.
> Jacky
>
>
> ------------------------------
>
> Message: 14
> Date: Thu, 20 Nov 2014 22:06:29 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] The error when install amber12+AmberTools13 on
> Ubuntucd
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <16BDE7B7-82CA-4CD2-B786-FFEA5A0D6BCA.gmail.com>
> Content-Type: text/plain; charset=utf-8
>
>
>> On Nov 20, 2014, at 9:31 PM, Biao Ma <jackyma1981.gmail.com> wrote:
>>
>> Hi, amber users.
>>
>> When I install the amber12 on my Ubuntu pc, I got the error messge when I
>> do 'make install'.
>> what I did is :
>>
>> #####################
>> # First time I did
>> #####################
>>
>> 1.
>>
>> sudo apt-get update
>> 2.
>>
>> sudo apt-get install csh flex patch gfortran g++ make xorg-dev
>> libbz2-dev
>> 3.
>>
>> sudo apt-get install python-tk python-dev python-matplotlib
>> python-numpy
>> python-scipy
>> 4.
>>
>> sudo apt-get install openmpi-bin libopenmpi-dev
>> 5.
>>
>> cd $AMBERHOME && make clean (the source files is copyed from another
>> Linux PC, which was successed installed amber by ./configure -mpi -rism
>> intel, make install)
>> 6.
>>
>> ./configure gnu
>> 7. make install (Error is out)
>>
>>
>>
>> the last part of stdout message after 'make install':
>>
>> cd ../lib && make nxtsec.o random.o
>> make[3]: Entering directory `/home/mabiao/bin/amber12/AmberTools/src/lib'
>> make[3]: `nxtsec.o' is up to date.
>> make[3]: `random.o' is up to date.
>> make[3]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src/lib'
>> cd ../lapack && make install
>> make[3]: Entering directory
>> `/home/mabiao/bin/amber12/AmberTools/src/lapack'
>> make[3]: Nothing to be done for `install'.
>> make[3]: Leaving directory
>> `/home/mabiao/bin/amber12/AmberTools/src/lapack'
>> cd ../blas && make install
>> make[3]: Entering directory
>> `/home/mabiao/bin/amber12/AmberTools/src/blas'
>> make[3]: Nothing to be done for `install'.
>> make[3]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src/blas'
>> cd ../arpack && make install
>> make[3]: Entering directory
>> `/home/mabiao/bin/amber12/AmberTools/src/arpack'
>> make[3]: Nothing to be done for `install'.
>> make[3]: Leaving directory
>> `/home/mabiao/bin/amber12/AmberTools/src/arpack'
>> gfortran -DFFTW -DBINTRAJ -ffree-form
>> -I/home/mabiao/bin/amber12/include -I/home/mabiao/bin/amber12/include
>> -o pbsa dsvdc.o pbsa.o pb_read.o pb_write.o getcoor.o runmd.o runmin.o
>> force.o pb_init.o sa_driver.o np_force.o pb_force.o pb_fddrv.o
>> pb_iimdrv.o
>> pb_nlsolver.o pb_exmol.o pb_mpfrc.o pb_direct.o pb_list.o timer.o
>> pb_fftsolv.o pb_fft.o egb.o ene.o locmem.o myopen.o rdparm.o pb_lsolver.o
>> decomp.o rgroup.o rfree.o debug.o coed20.o indexg.o irre32.o phidev.o
>> project.o qld.o coed6.o irre31.o miniop.o iimod.o prodis.o qint.o
>> wint.o transf.o curv.o GrToPr.o jumps.o problem.o IIM.o regular.o
>> gmres.o
>> daxpy.o ddot.o dheqr.o dpigmr.o dscal.o dslui2.o dxlcal.o
>> dchkw.o
>> dgmres.o dnrm2.o drlcal.o dsilus.o dslui.o isdgmr.o dcopy.o
>> dhels.o
>> dorth.o ds2y.o dslugm.o dsmv.o qs2i1d.o d1mach.o fdump.o
>> i1mach.o j4save.o xercnt.o xerhlt.o xermsg.o xerprn.o xersve.o
>> xgetua.o bicg.o dbcg.o dslui4.o dsluti.o dsmtv.o dslubc.o isdbcg.o
>> pb_chkfrc.o svdcmp.o svbksb.o pythag.o pb_augdrv.o gmresX.o interpX.o
>> matvec3.o gen_dx_file.o aug_iccg.o membrane.o fftw3.o \
>> ../lib/nxtsec.o ../lib/random.o -lfftw3 \
>> -L/home/mabiao/bin/amber12/lib -larpack -llapack -lblas
>> /usr/bin/ld: skipping incompatible
>> /home/mabiao/bin/amber12/lib/libfftw3.a
>> when searching for -lfftw3
>> /usr/bin/ld: cannot find -lfftw3
>> collect2: error: ld returned 1 exit status
>> make[2]: *** [pbsa] Error 1
>> make[2]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src/pbsa'
>> make[1]: *** [serial] Error 2
>> make[1]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src'
>> make: *** [install] Error 2
>>
>> when I check the folder ~/amber12/lib/ I found some older files was
>> created
>> at 2013,
>> -rw-r--r-- 1 mabiao mabiao 3.0M Nov 28 2013 libfftw3.a
>> -rw-r--r-- 1 mabiao mabiao 80K Nov 28 2013 libxblas-amb.a
>> -rw-r--r-- 1 mabiao mabiao 1.2M Nov 28 2013 libnab.a
>> -rw-r--r-- 1 mabiao mabiao 1.6M Nov 28 2013 libnetcdf.a
>> -rwxr-xr-x 1 mabiao mabiao 898 Nov 20 15:02 libDiagnostics.la
>> -rw-r--r-- 1 mabiao mabiao 5.8K Nov 20 15:02 libDiagnostics.a
>> -rwxr-xr-x 1 mabiao mabiao 886 Nov 20 15:02 libtinyxml.la
>> -rw-r--r-- 1 mabiao mabiao 120K Nov 20 15:02 libtinyxml.a
>>
>> why the old file not removed when 'make clean??
>
> Because they shouldn?t be. This is a task for ?make uninstall?, not ?make
> clean? (if ?make clean? got rid of these files, then ?make clean? would
> effectively uninstall Amber each time!)
>
>>
>> #####################
>> # second time I did
>> #####################
>>
>> I try to delete all the files in $AMBERHOME/lib/, and then do
>> make clean
>> ./configure gnu
>> make install
>>
>> this time I got the another error message
>>
>> gcc: error: /home/mabiao/bin/amber12/lib/libnetcdf.a: No such file or
>> directory
>> make[2]: *** [rdparm] Error 1
>> make[2]: Leaving directory
>> `/home/mabiao/bin/amber12/AmberTools/src/ptraj'
>> make[1]: *** [serial] Error 2
>> make[1]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src'
>> make: *** [install] Error 2
>>
>> I check the $AMBERHOME/lib/ folder and found there no libnetcdf.a ,
>>
>> The files in $AMBERHOME/lib/ folder how to be generated ?
>> Who can give me some advice ?
>
> Upgrade to AmberTools 14, or start from a fresh copy of AmberTools 12 +
> Amber 12.
>
> If that?s not plausible, run the command ?make clean uninstall? and try to
> start from there.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
>
> ------------------------------
>
> Message: 15
> Date: Fri, 21 Nov 2014 12:47:49 +0530
> From: Robin Jain <robinjain.chem.gmail.com>
> Subject: [AMBER] cut value in minimisation
> To: amber <amber.ambermd.org>
> Message-ID:
> <CA+QHj+n1W2HGvxhPwEJVe=MDS7vB7f_FVqo7H=T_G_CZn9HtEA.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear all,
> I am minimising my system in a cubic box of 17.58 A using sander. for
> this what value of cut must be used so that periodic boundary
> condition remain constant . Since i used 8 A value but the program
> still stop with an error, so please help me in this regard.
> Thanking You.
> --
> Robin Jain
>
>
>
> ------------------------------
>
> Message: 16
> Date: Fri, 21 Nov 2014 15:38:52 +0800 (GMT+08:00)
> From: "Liu, Hui" <hl.zju.edu.cn>
> Subject: [AMBER] Bug Report
> To: amber.ambermd.org
> Message-ID: <206ae23a.11261.149d14a0fd0.Coremail.hl.zju.edu.cn>
> Content-Type: text/plain; charset=GBK
>
> Hi,
>
> I found a little bug in AMBER14. It makes the update fail when a local
> directory is specified and the path starts with "file:///".
>
> In amber14/updateutils/repos.py, line 321:
> " self.location = self.location.replace('', 'file://')"
> It should be:
> " self.location = self.location.replace('file://', '')"
>
> Hui Liu
>
>
>
>
> ------------------------------
>
> Message: 17
> Date: Fri, 21 Nov 2014 05:18:44 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] cut value in minimisation
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <B8AE5C40-F73D-4876-9F87-510168830E4C.gmail.com>
> Content-Type: text/plain; charset=utf-8
>
>
>> On Nov 21, 2014, at 2:17 AM, Robin Jain <robinjain.chem.gmail.com> wrote:
>>
>> Dear all,
>> I am minimising my system in a cubic box of 17.58 A using sander. for
>> this what value of cut must be used so that periodic boundary
>> condition remain constant .
>
> The cutoff has no effect on the box size. In fact, the only thing that can
> change the box size is a constant pressure simulation (which is _supposed_
> to change the box size). I would suggest just using 8 A or something close
> to that.
>
> Why do you continue to think that your box size keeps changing due to
> different settings?
>
>> Since i used 8 A value but the program
>> still stop with an error, so please help me in this regard.
>
> Change the setting causing an error so that the error doesn?t occur.
>
> That is the best help anyone provide given this information. What was the
> exact error message you got? What was the input that you used? Did you
> google the error message to see if someone has encountered the problem
> before? What did you do to try and fix the problem?
>
> Be specific, and give exact input and output, but only the parts that are
> actually relevant to reproducing and/or diagnosing your problem.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
>
> ------------------------------
>
> Message: 18
> Date: Fri, 21 Nov 2014 05:30:30 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Bug Report
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <E8102AA0-5F33-46EA-BCC9-455B6C1ADC26.gmail.com>
> Content-Type: text/plain; charset=utf-8
>
> Thanks for the report. I?ve made the change.
>
> There should be some simple workarounds here. The only way you should
> encounter this problem is if you are setting up a local mirror to a folder
> where you download all of the updates.
>
> In this case, you can set the mirror using update_amber with a command like
>
> ?./update_amber --amber-updates /path/to/amber/updates?
>
> or
>
> ?./update_amber --ambertools-updates /path/to/amber/updates?
>
> In this case, there is no need to specify ?file:///path/to/amber/updates
> <file:///path/to/amber/updates>? -- it recognizes local folders just fine.
>
> Alternatively, you can make this fix by hand. I won?t release an update for
> the script, since the workarounds here are easy and the bug itself is
> unlikely to affect more people (and the side-effects of an update to
> update_amber are worse than this bug, IMO.
>
> Thanks again for the report!
> Jason
>
>> On Nov 21, 2014, at 2:38 AM, Liu, Hui <hl.zju.edu.cn> wrote:
>>
>> Hi,
>>
>> I found a little bug in AMBER14. It makes the update fail when a local
>> directory is specified and the path starts with "file:///".
>>
>> In amber14/updateutils/repos.py, line 321:
>> " self.location = self.location.replace('', 'file://')"
>> It should be:
>> " self.location = self.location.replace('file://', '')"
>>
>> Hui Liu
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
>
> ------------------------------
>
> Message: 19
> Date: Fri, 21 Nov 2014 10:43:50 +0000
> From: Maria Diaz <mddiazhdez.yahoo.com>
> Subject: [AMBER] cyclic peptide side chains
> To: amber.ambermd.org
> Message-ID:
> <1416566630.14987.YahooMailBasic.web172202.mail.ir2.yahoo.com>
> Content-Type: text/plain; charset=utf-8
>
> Hi,
>
> we want to carry out MD simulations for a cyclic peptide using amber. The
> cyclic peptide we are currently study has a bond between (modified) side
> chains of two amino acids (i.e. N-terminus or first amino acid and sixth
> residue). How can I parametrized the modified residues?
> I would appreciate very much any help and suggestion
> Thank you very much for your consideration
>
>
>
>
>
> ------------------------------
>
> Message: 20
> Date: Fri, 21 Nov 2014 19:12:07 +0800
> From: "m13654940810"<m13654940810.163.com>
> Subject: [AMBER] about nab
> To: "amber"<amber.ambermd.org>
> Message-ID: <571d16ae.54d9.149d2042429.Coremail.m13654940810.163.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello,
> I want to use NAB to build a single nucleotide with capped 5'(phosphate)?I
> wonder how to do it?
> thank you in advance.
> guowei
> 2014-11-21
>
>
> m13654940810
>
> ------------------------------
>
> Message: 21
> Date: Fri, 21 Nov 2014 07:26:26 -0500
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] cut value in minimisation
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20141121122626.GD21531.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Fri, Nov 21, 2014, Robin Jain wrote:
>
>> I am minimising my system in a cubic box of 17.58 A using sander. for
>> this what value of cut must be used so that periodic boundary
>> condition remain constant . Since i used 8 A value but the program
>> still stop with an error, so please help me in this regard.
>
> As Jason pointed out, providing the actual error message would be a great
> help.
>
> Generally, the box size must be greater than 2*cutoff + skinnb, where
> skinnb
> is a buffer region that allows the nonbonded list to be updated less
> frequently. It's default is 2 Ang, which (I'm guessing!) is what is
> causing
> your error.
>
> You *could* reduce skinnb to 1 Ang. But 17.5 Ang is a very small box size
> for
> Amber calculations. So you should also consider going to a bigger system.
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 22
> Date: Fri, 21 Nov 2014 07:29:02 -0500
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] cyclic peptide side chains
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20141121122902.GE21531.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Fri, Nov 21, 2014, Maria Diaz wrote:
>
>>
>> we want to carry out MD simulations for a cyclic peptide using
>> amber. The cyclic peptide we are currently study has a bond between
>> (modified) side chains of two amino acids (i.e. N-terminus or first
>> amino acid and sixth residue). How can I parametrized the modified
>> residues?
>
> For the "antechamber" route to developing parameters for modified amino
> acids,
> see both tutorial B4, and this page:
>
> http://ambermd.org/antechamber/pro4.html
>
> You might also want to use the R.E.D. server: see the link at the Amber web
> page.
>
> ...good luck....dac
>
>
>
>
> ------------------------------
>
> Message: 23
> Date: Fri, 21 Nov 2014 07:36:23 -0500
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] about nab
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20141121123623.GF21531.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=utf-8
>
> On Fri, Nov 21, 2014, m13654940810 wrote:
>
>> I want to use NAB to build a single nucleotide with capped
>> 5'(phosphate)?I wonder how to do it?
>
> See note 6 in Section 3.1 of the Amber14 Reference Manual. Note that the
> deprotonated phosphate version (2- charge) is not in the standard library,
> so
> you would have to treat this as a new residue, probably using R.E.D. to
> assist
> in getting the charges.
>
> ...good luck...dac
>
>
>
>
> ------------------------------
>
> Message: 24
> Date: Fri, 21 Nov 2014 10:18:00 -0500
> From: Pengfei Li <ambermailpengfei.gmail.com>
> Subject: Re: [AMBER] Help generating Heme parameters
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <1B23706A-E0B2-4E44-91D2-A91FC35899C9.gmail.com>
> Content-Type: text/plain; charset=utf-8
>
> Hi Junaid,
>
> If you want to use MCPB to deal with it, you need to have prep file of the
> system first (do RESP charge calculation using Gaussian, and
> then use antechamber to generate the prep file, I recommend you to have the
> atom type in AMBER atom type) and then you can use
> prep2xml to transfer the file into xml format, in which MCPB can recognize
> it. Then you can read the xml as lib file and do the normal
> MCPB steps. It may contain a lot of trial and error process during the
> modeling.
>
> Another way to deal with it is to define the bond, angle parameters by using
> a empirical way (and the charge still in RESP way),
> in which you can check the former literatures, pick meaningful values and
> apply it in your system.
>
> You can send me the structure file and I can help to look at it.
>
> Best,
> Pengfei
>
> On Nov 19, 2014, at 2:20 AM, ?? <junaid.hust.edu.cn> wrote:
>
>> Dear Amber Users
>>
>> I wan t to simulate the complex that contain Heme group using Amber14. We
>> have got some problem in generating Heme parameters. The contributing
>> parameters for Heme is for the Heme group attached to Histidine . But in
>> our case the Heme is attached to Cysteine. We tried the MCPB function in
>> Amber14 but the tutorial is not suitable for Heme, because in Heme the
>> metal is not surrounded by amino acid residues.
>> So i have attached the pdb file for Heme and associated to Cysteine. Could
>> someone generate parameters or give some instructions on how to do it.
>> Any help will be highly appreciated!!!
>>
>> Junaid
>> <Heme_cysteine.pdb>_______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 25
> Date: Fri, 21 Nov 2014 13:15:02 -0500
> From: Jonathan Gough <jonathan.d.gough.gmail.com>
> Subject: [AMBER] Issues with Cholesterol lipid11, lipid14 and
> lipid14_supp.lib
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAFkCv1RJOPzrGQtMZfoSRWpawCUj9RKpqRda1+JF+vgXVVG-=g.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi All,
>
> I'm a bit confused and not really sure what is going on.
>
> Using
>
> AmberTools version 14.12
> Amber version 14.06
>
> I'm trying to simulate a POPC/Cholesterol/protein system.
>
> My understanding was that any parm missing from lipid14 could be used
> by loading the lipid14_supp.lib.
>
> However, Cholesterol (CHL) param can't be generated. Specifically,
> leap kicks out the error that it can't find and vdW parameters for H
> or O.
>
> for example:
> For atom: .R<CHL 352>.A<H11 2> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H12 3> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H21 5> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H22 6> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H41 10> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H42 11> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H71 16> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H72 17> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H81 19> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H91 21> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H111 24> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H112 25> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H121 27> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H122 28> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H141 31> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H151 33> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H152 34> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H161 36> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H162 37> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H171 39> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H181 41> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H182 42> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H183 43> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H191 45> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H192 46> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H193 47> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H201 49> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H211 51> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H212 52> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H213 53> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H221 55> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H222 56> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H231 58> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H232 59> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H241 61> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H242 62> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H251 64> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H261 66> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H262 67> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H263 68> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H271 70> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H272 71> Could not find vdW (or other)
> parameters for type: hA
> For atom: .R<CHL 352>.A<H273 72> Could not find vdW (or other)
> parameters for type: hA
>
>
> leap can build CHL and the appropriate .lib .prmtop .inpcrd using lipid11.
>
> Even if I load the CHL.lib created with lipid11 (via leap) I can't use
> it with lipid14 parm (I get the same vdW errors). I'm really
> confused...
>
> comparing the lipid11.lib and lipid14_supp.lib I can't seem to find
> any difference between the 2 CHL entries (via diff).
>
> any insight or help would be greatly appreciated.
>
> Thanks,
> Jonathan
>
>
>
> ------------------------------
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 1045, Issue 1
> **************************************
>
--
Robin Jain
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 22 2014 - 00:30:03 PST
