SORRY FOR MY LAST POSTING. DID NOT CHANGE THE SUBJECT TITLE.
Dear Bill,
Thank you for responding. Well my system comprises of 190
residues with a total of 3112 atoms. I believe this is still a
relatively small system and I am performing the calculation in only 2
frames. So I am expecting this not to take so long (>10 hours of CPU
time).
Ok the long calculation time is one problem. The other problem is that
I am getting an Index error as mentioned below.
--------------------------------------------------------------
Traceback (most recent call last):
File
"/cluster/apps/x86_64/packages/amber11-patch-19/src/AmberTools/src/mmpbsa_py/MMPBSA.py", line 1344, in
<module>
outfile.write(str(nmodenorm))
File
"/cluster/apps/x86_64/packages/amber11-patch-19/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py", line 2263, in
__str__
totavg, totstdev = self.AvgStdev()
File
"/cluster/apps/x86_64/packages/amber11-patch-19/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py", line 2302, in
AvgStdev
stdev = self._tot_stdevs()
File
"/cluster/apps/x86_64/packages/amber11-patch-19/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py", line 2319, in
_tot_stdevs
sum += self.com_data[0][i] - self.rec_data[0][i] - self.lig_data[0][i]
IndexError: list index out of range
--------------------------------------------------------------------
I went through the mailing list to get an idea and people seem to have
this error message. Some have issues with defining the receptor or
ligand mask whereas other discussion is around Bugfix.
I think my issue is not with defining the mask as I can see from the
output file that the program has rightly guessed the receptor and
ligand mask.
-------------------------------------------------------------
|Input file:
|--------------------------------------------------------------
|sample input file for NMODE calculation
|&general
|startframe=1, endframe=10, interval=5,
|verbose=1, keep_files=0, strip_mdcrd=0,
|/
|&nmode
|dielc=1.0,
|nmstartframe=1, nmendframe=2, nminterval=1,
|maxcyc=10000, drms=0.001,
|nmode_igb=1, nmode_istrng=0.1,
|/
|--------------------------------------------------------------
|Complex topology file: ../complex.parmtop
|Receptor topology file: ../protein.parmtop
|Ligand topology file: ../ligand.parmtop
|Initial mdcrd(s): ../../centering/prod_cen_strip_sol_ion.mdcrd
|
|Best guess for receptor mask: ":1-189"
|Best guess for ligand mask: ":190"
|Ligand residue name is "MGO"
|
|Calculations performed using 2 frames.
|NMODE calculations performed using 2 frames.
|
|All units are reported in kcal/mole.
|All entropy results have units kcal/mole (Temperature is 298.15 K).
-------------------------------------------------------------------------------
Well so what could be the possible reason? Can someone please help me
out with both these issues.
1) The long time for NMODE calculation with MMPBSA.py and
2) The Index error.
Thank you,
Dilraj.
[Show Quoted Text - 57 lines][Hide Quoted Text]
Message: 5
Date: Fri, 14 Sep 2012 16:54:37 +0800
From: Dilraj LAMA <dilrajl.bii.a-star.edu.sg>
Subject: [AMBER] NMODE calculation using mmpbsa.py
To: amber.ambermd.org
Message-ID:
<20120914165437.160673zz3c9psjwt.webmail.bii.a-star.edu.sg>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
format="flowed"
Dear Amber users,
I am trying to use the python script for MMPBSA
calculation. As a test, I am running the calculation on two snapshot
from my trajectory. The PB and GB calculation went of fine but am
having issues with the NMODE calculation.
It is taking unusually long time to perform the calculation (close to
10hours of CPU time)
Here is my input script.
--------------------------------------
sample input file for NMODE calculation
&general
startframe=1, endframe=10, interval=5,
verbose=1, keep_files=0, strip_mdcrd=0,
/
&nmode
dielc=1.0,
nmstartframe=1, nmendframe=2, nminterval=1,
maxcyc=10000, drms=0.001,
nmode_igb=1, nmode_istrng=0.1,
/
--------------------------------------
I am using the serial version of MMPBSA.py.
Its just a two frame calculation, So shouldn't take that long.
Am I missing something? Will be glad if someone give me an insight.
Thank you,
Dilraj.
Message: 7
Date: Fri, 14 Sep 2012 07:15:28 -0400
From: Bill Miller III <brmilleriii.gmail.com>
Subject: Re: [AMBER] NMODE calculation using mmpbsa.py
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <E20FEF81-A83F-4FC5-8F2E-8E37B33AE0D1.gmail.com>
Content-Type: text/plain; charset=us-ascii
Nmode calculations are very computationally demanding and could easily
take this long depending on system size and available computer
resources. Without knowing these details, though, it is difficult to
assess whether this is expected or not for your calculation.
-Bill
Quoting amber-request.ambermd.org:
> Send AMBER mailing list submissions to
> amber.ambermd.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.ambermd.org/mailman/listinfo/amber
> or, via email, send a message with subject or body 'help' to
> amber-request.ambermd.org
>
> You can reach the person managing the list at
> amber-owner.ambermd.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of AMBER digest..."
>
>
> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: Cpptraj - Autoimage (Thomas Cheatham III)
> 2. Help for rdf (Yanyan ZHU)
> 3. Re: Error in converstion of pdb to mol2 (Anogna)
> 4. MMPBSA: standard deviation (George Tzotzos)
> 5. NMODE calculation using mmpbsa.py (Dilraj LAMA)
> 6. Re: MMPBSA: standard deviation (Hannes Loeffler)
> 7. Re: NMODE calculation using mmpbsa.py (Bill Miller III)
> 8. GAFFLipid Parameters (Gould, Ian R)
> 9. Re: MMPBSA: standard deviation (Jason Swails)
> 10. Re: GAFFLipid Parameters (Albert)
> 11. query antechamber-reg (Revthi Sanker)
> 12. Re: GAFFLipid Parameters (Dickson, Callum)
> 13. Re: GAFFLipid Parameters (Albert)
> 14. Re: GAFFLipid Parameters (Dickson, Callum)
> 15. Re: GAFFLipid Parameters (Adrian Roitberg)
> 16. Re: GAFFLipid Parameters (Dickson, Callum)
> 17. Re: GAFFLipid Parameters (Adrian Roitberg)
> 18. Re: query antechamber-reg (David A Case)
> 19. Re: Error in converstion of pdb to mol2 (David A Case)
> 20. Re: POL3 water model run error... (David A Case)
> 21. Re: GAFFLipid Parameters (Albert)
> 22. Re: GAFFLipid Parameters (Ross Walker)
> 23. Re: Antibiotics Parameters (Shahoei, Seyyedehrezvan)
> 24. performance of pmed.cuda.MPI (Jonathan Gough)
> 25. Re: performance of pmed.cuda.MPI (Scott Le Grand)
> 26. Re: performance of pmed.cuda.MPI (Jonathan Gough)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 13 Sep 2012 13:17:55 -0600 (Mountain Daylight Time)
> From: Thomas Cheatham III <tec3.utah.edu>
> Subject: Re: [AMBER] Cpptraj - Autoimage
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <alpine.WNT.2.00.1209131314040.6496.guanine>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
>
>
>> That's exactly the problem. And no, there isn't any problem with
>> ccptraj according to this.
>>
>> Yes, we have been made this option you suggest, but we wanted to skip
>> these steps, avoiding the equilibration of the box again. I know it's
>> difficult what I propose, but only to know if cpptraj had this option.
>
> There is no way you can rotate a single unit cell in a periodic
> orthorhombic box; it would bump into its images. You can rotate the
> entire periodic system, but this will not do what you want (i.e. orient
> the molecule along the long axis). If you are concerned about
> re-equilibration, either start with a large enough more spherical box
> (truncated octahedron) or you will have to re-solvate. Programs like
> PackMol may do a better job of initially solvating. If you really need
> long rectangular box you may have to restrain the system to keep it
> oriented along the long axis as natural molecule rotation on nanoseconds
> time scales is expected... --tec3
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 14 Sep 2012 11:23:19 +0800
> From: Yanyan ZHU <zhuyanzily.gmail.com>
> Subject: [AMBER] Help for rdf
> To: amber.ambermd.org
> Message-ID:
> <CAMR4AgzVEGp1qqWki+t-rCHtro7zQiq1C+=t3M_yf=_bBTiNMw.mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear all:
> I have received your reply and very grateful for your help. However,
> I have some other puzzles that I have sent as enclosure. I am looking for
> your reply .Give my best wishs to you.
>
>
> 2012.09.14
>
>
>
> yanyan,zhu
> -------------- next part --------------
> A non-text attachment was scrubbed...
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> http://lists.ambermd.org/mailman/private/amber/attachments/20120914/a747140b/attachment-0001.pdf
>
> ------------------------------
>
> Message: 3
> Date: Fri, 14 Sep 2012 10:48:06 +0530
> From: Anogna <anognal.gmail.com>
> Subject: Re: [AMBER] Error in converstion of pdb to mol2
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAG-gr8E6Ov-J+kn+E+GhzqsyTL-7bXN7yo9NnDBWSjHie+s6qA.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi
>
> The following is my ligand pdb file
>
> REMARK Created: Thu Sep 13 11:10:12 India Standard Time 2012
> HETATM 8833 C1 COM A 1 19.831 16.769 69.471 1.00 0.00
> C
> HETATM 8834 C2 COM A 1 20.941 17.638 69.469 1.00 0.00
> C
> HETATM 8835 C3 COM A 1 19.620 15.877 68.404 1.00 0.00
> C
> HETATM 8836 C4 COM A 1 21.863 17.622 68.383 1.00 0.00
> C
> HETATM 8837 C5 COM A 1 20.523 15.850 67.326 1.00 0.00
> C
> HETATM 8838 C6 COM A 1 21.633 16.717 67.318 1.00 0.00
> C
> HETATM 8839 C7 COM A 1 23.070 18.532 68.329 1.00 0.00
> C
> HETATM 8840 O8 COM A 1 24.030 18.214 67.593 1.00 0.00
> O
> HETATM 8841 O9 COM A 1 21.089 18.480 70.534 1.00 0.00
> O
> HETATM 8842 N10 COM A 1 20.326 15.002 66.307 1.00 0.00
> N
> HETATM 8843 O17 COM A 1 23.087 19.579 69.016 1.00 0.00
> O
> TER
> END
>
>
> can u plz verify if and suggest me is any problem in my pdb file that
> causing me the error as I mentioned in my previous msg.
>
> On Thu, Sep 13, 2012 at 5:17 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> My suggestion is to upgrade to AmberTools 12 and use antechamber from
>> there. If you are still having problems, it'll be easier to help.
>> (segfaults are hard to diagnose in our own programs, let alone such a
>> complicated one as mopac that we don't actually develop and haven't used in
>> years).
>>
>> HTH,
>> Jason
>>
>> On Thu, Sep 13, 2012 at 2:03 AM, Anogna <anognal.gmail.com> wrote:
>>
>> > Dear David,
>> >
>> > I tried to regenerate the mol2 file using -nc flag
>> >
>> > I used:
>> > antechamber -i lgn_h.pdb -fi pdb -o lgn.mol2 -fo mol2 -c bcc -nc 1 -j 5
>> >
>> > Error was:
>> >
>> > Total number of electrons: 72; net charge: 1
>> >
>> > Running: /applications/smp/amber/10/intelmpi-mkl/bin/mopac.sh
>> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> > Image PC Routine Line
>> Source
>> > mopac 40000000000FA490 Unknown Unknown
>> Unknown
>> > mopac 4000000000101900 Unknown Unknown
>> Unknown
>> > mopac 4000000000044A30 Unknown Unknown
>> Unknown
>> > mopac 40000000000B5870 Unknown Unknown
>> Unknown
>> > mopac 40000000000141F0 Unknown Unknown
>> Unknown
>> > mopac 4000000000003350 Unknown Unknown
>> Unknown
>> > libc.so.6.1 2000000000407D60 Unknown Unknown
>> Unknown
>> > mopac 4000000000003180 Unknown Unknown
>> Unknown
>> > Error: unable to find mopac charges in mopac.out
>> >
>> > Can u plz help me out of this.
>> >
>> >
>> > Regards,
>> > Anogna
>> >
>> > On Wed, Sep 12, 2012 at 6:18 PM, David A Case <case.biomaps.rutgers.edu
>> > >wrote:
>> >
>> > > On Wed, Sep 12, 2012, Anogna wrote:
>> > > >
>> > > > I tried to convert my ligand pdb file to Mol2 file using antechamber.
>> > > >
>> > > > Total number of electrons: 79; net charge: 0
>> > > > INFO: Number of electrons is odd: 79
>> > > > Please check the total charge (-nc flag) and spin multiplicity
>> > (-m
>> > > > flag)
>> > >
>> > > Antechamber can only deal with closed-shell molecules with an even
>> number
>> > > of
>> > > electrons. Check your pdb file to make sure it is correct (with all
>> > > hydrogens
>> > > present in good locations). If the molecule has a charge other than
>> > zero,
>> > > you
>> > > have to use the "-nc" flag.
>> > >
>> > > >
>> > > > Running: /applications/smp/amber/10/intelmpi-mkl/bin/mopac.sh
>> > > > *** glibc detected ***
>> > /applications/smp/amber/10/intelmpi-mkl/bin/mopac:
>> > > > malloc(): memory corruption: 0x60000000046fc1a0 ***
>> > > > ======= Backtrace: =========
>> > > > /lib/libc.so.6.1[0x20000000004af090]
>> > >
>> > > Make sure the test cases pass: it looks like you might have a
>> > > non-functional
>> > > version of mopac. Consider upgrading AmberTools to a more current
>> > version.
>> > >
>> > > ...good luck....dac
>> > >
>> > >
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> >
>> >
>> >
>> > --
>> > ...........INDIA is great
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> ...........INDIA is great
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 14 Sep 2012 10:28:07 +0200
> From: George Tzotzos <gtzotzos.me.com>
> Subject: [AMBER] MMPBSA: standard deviation
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <19BC6168-3518-4C4E-8639-C1160CBB8F3A.me.com>
> Content-Type: text/plain; CHARSET=US-ASCII
>
> For a large number of DELTA G binding (Complex - Receptor - Ligand)
> the standard deviation is > 2 when DELTA G is ~30kcal/mol
>
> Translating DELTA G to dissociation constant, a 2kcal/mol difference
> (either way) would mean dissociation constants differing by two
> orders of magnitude from the mean.
>
> To put it in a different way. If DELTA G binding for ligand 1 to
> receptor A is 30kcal/mol and DELTA G binding of ligand 2 to the same
> receptor is 28kcal/mol with a standard deviation of 2, can one infer
> that the receptor has higher binding affinity for ligand 1?
>
> Furthermore, if one factors in DELTA S with SD 2 (or more)
> interpretation of the results becomes much more tenuous.
>
> And last, but not least. I have obtained standard deviations varying
> between 2 and 5 for nmode DELTA S calculations involving different
> ligands with the same receptor but the same number of frame
> readings. Is this to be expected?
>
> Looking forward to receiving any comments on the above,
>
> Regards
>
> George
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 14 Sep 2012 16:54:37 +0800
> From: Dilraj LAMA <dilrajl.bii.a-star.edu.sg>
> Subject: [AMBER] NMODE calculation using mmpbsa.py
> To: amber.ambermd.org
> Message-ID:
> <20120914165437.160673zz3c9psjwt.webmail.bii.a-star.edu.sg>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> Dear Amber users,
> I am trying to use the python script for MMPBSA
> calculation. As a test, I am running the calculation on two snapshot
> from my trajectory. The PB and GB calculation went of fine but am
> having issues with the NMODE calculation.
>
> It is taking unusually long time to perform the calculation (close to
> 10hours of CPU time)
>
> Here is my input script.
>
> --------------------------------------
> sample input file for NMODE calculation
> &general
> startframe=1, endframe=10, interval=5,
> verbose=1, keep_files=0, strip_mdcrd=0,
> /
> &nmode
> dielc=1.0,
> nmstartframe=1, nmendframe=2, nminterval=1,
> maxcyc=10000, drms=0.001,
> nmode_igb=1, nmode_istrng=0.1,
> /
> --------------------------------------
> I am using the serial version of MMPBSA.py.
>
> Its just a two frame calculation, So shouldn't take that long.
>
> Am I missing something? Will be glad if someone give me an insight.
>
> Thank you,
> Dilraj.
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 14 Sep 2012 09:58:43 +0100
> From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
> Subject: Re: [AMBER] MMPBSA: standard deviation
> To: <amber.ambermd.org>
> Message-ID: <20120914095843.4e77564b.zgb83773vig.dl.ac.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> A standard deviation (I would think correctly that's the SD of and
> not from the mean i.e. the standard error) implies that you assume a
> Gaussian distribution with a shape determined by SD. So actually you
> are comparing two probability distributions. My first thought would be
> that their overlap would give you a hint as to how significant the
> difference (another probability) is. Of course, all your statistics is
> estimated from what you already have and one typically assumes that this
> is representative for the property under study,,,
>
> Has DELTA S been calculated to the "same" quality as DELTA G? I would
> think that the entropy is much harder to catch than the energy.
>
>
> On Fri, 14 Sep 2012 10:28:07 +0200
> George Tzotzos <gtzotzos.me.com> wrote:
>
>> For a large number of DELTA G binding (Complex - Receptor - Ligand)
>> the standard deviation is > 2 when DELTA G is ~30kcal/mol
>>
>> Translating DELTA G to dissociation constant, a 2kcal/mol difference
>> (either way) would mean dissociation constants differing by two
>> orders of magnitude from the mean.
>>
>> To put it in a different way. If DELTA G binding for ligand 1 to
>> receptor A is 30kcal/mol and DELTA G binding of ligand 2 to the same
>> receptor is 28kcal/mol with a standard deviation of 2, can one infer
>> that the receptor has higher binding affinity for ligand 1?
>>
>> Furthermore, if one factors in DELTA S with SD 2 (or more)
>> interpretation of the results becomes much more tenuous.
>>
>> And last, but not least. I have obtained standard deviations varying
>> between 2 and 5 for nmode DELTA S calculations involving different
>> ligands with the same receptor but the same number of frame readings.
>> Is this to be expected?
> --
> Scanned by iCritical.
>
>
>
> ------------------------------
>
> Message: 7
> Date: Fri, 14 Sep 2012 07:15:28 -0400
> From: Bill Miller III <brmilleriii.gmail.com>
> Subject: Re: [AMBER] NMODE calculation using mmpbsa.py
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <E20FEF81-A83F-4FC5-8F2E-8E37B33AE0D1.gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Nmode calculations are very computationally demanding and could
> easily take this long depending on system size and available
> computer resources. Without knowing these details, though, it is
> difficult to assess whether this is expected or not for your
> calculation.
>
> -Bill
>
>
>
> On Sep 14, 2012, at 4:54 AM, Dilraj LAMA <dilrajl.bii.a-star.edu.sg> wrote:
>
>> Dear Amber users,
>> I am trying to use the python script for MMPBSA
>> calculation. As a test, I am running the calculation on two snapshot
>> from my trajectory. The PB and GB calculation went of fine but am
>> having issues with the NMODE calculation.
>>
>> It is taking unusually long time to perform the calculation (close to
>> 10hours of CPU time)
>>
>> Here is my input script.
>>
>> --------------------------------------
>> sample input file for NMODE calculation
>> &general
>> startframe=1, endframe=10, interval=5,
>> verbose=1, keep_files=0, strip_mdcrd=0,
>> /
>> &nmode
>> dielc=1.0,
>> nmstartframe=1, nmendframe=2, nminterval=1,
>> maxcyc=10000, drms=0.001,
>> nmode_igb=1, nmode_istrng=0.1,
>> /
>> --------------------------------------
>> I am using the serial version of MMPBSA.py.
>>
>> Its just a two frame calculation, So shouldn't take that long.
>>
>> Am I missing something? Will be glad if someone give me an insight.
>>
>> Thank you,
>> Dilraj.
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 8
> Date: Fri, 14 Sep 2012 11:21:36 +0000
> From: "Gould, Ian R" <i.gould.imperial.ac.uk>
> Subject: [AMBER] GAFFLipid Parameters
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID:
> <9287702E516D4A43A55B9596C4AA64A530106146.icexch-m6.ic.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear All,
>
> We have just uploaded our GAFFlipid parameters and other associated
> files to LipidBook:
>
> http://lipidbook.bioch.ox.ac.uk/
>
> If you use our parameters please remember to cite our paper.
>
> Callum J. Dickson , Lula Rosso , Robin M. Betz , Ross C. Walker and
> Ian R. Gould, GAFFlipid: a General Amber Force Field for the
> accurate molecular dynamics simulation of phospholipid, Soft Matter
> 8 (2012), 9617-9627, doi:
> 10.1039/C2SM26007G<http://dx.doi.org/10.1039/C2SM26007G>
>
> They will also be available from the amber parameter database
> maintained by Richard Bryce at Manchester in due course.
>
> Cheers
> Ian
>
> Women love us for our defects. If we have enough of them, they will
> forgive us everything, even our intellects.
> Oscar Wilde,
> --
> Dr Ian R Gould
> Reader in Computational Chemical Biology
> Department of Chemistry
> Imperial College London
> Exhibition Road
> London
> SW7 2AY
> E-mail i.gould.imperial.ac.uk
> http://www3.imperial.ac.uk/people/i.gould
> Tel +44 (0)207 594 5809
>
>
> ------------------------------
>
> Message: 9
> Date: Fri, 14 Sep 2012 07:43:39 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] MMPBSA: standard deviation
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3pY--PneE2WscNmbUmaaGA40hRRjYdBBQRpSR1FE9CkTw.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> I wrote a rather lengthy expose on MM/PBSA and errors/fluctuations back in
> February. In the interest if not repeating myself, I'll simply provide a
> link to it:
>
> http://archive.ambermd.org/201202/0317.html
>
> HTH,
> Jason
>
> On Fri, Sep 14, 2012 at 4:28 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> For a large number of DELTA G binding (Complex - Receptor - Ligand) the
>> standard deviation is > 2 when DELTA G is ~30kcal/mol
>>
>> Translating DELTA G to dissociation constant, a 2kcal/mol difference
>> (either way) would mean dissociation constants differing by two orders of
>> magnitude from the mean.
>>
>> To put it in a different way. If DELTA G binding for ligand 1 to receptor
>> A is 30kcal/mol and DELTA G binding of ligand 2 to the same receptor is
>> 28kcal/mol with a standard deviation of 2, can one infer that the receptor
>> has higher binding affinity for ligand 1?
>>
>> Furthermore, if one factors in DELTA S with SD 2 (or more) interpretation
>> of the results becomes much more tenuous.
>>
>> And last, but not least. I have obtained standard deviations varying
>> between 2 and 5 for nmode DELTA S calculations involving different ligands
>> with the same receptor but the same number of frame readings. Is this to be
>> expected?
>>
>> Looking forward to receiving any comments on the above,
>>
>> Regards
>>
>> George
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
>
> ------------------------------
>
> Message: 10
> Date: Fri, 14 Sep 2012 14:39:25 +0200
> From: Albert <mailmd2011.gmail.com>
> Subject: Re: [AMBER] GAFFLipid Parameters
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <5053257D.3020404.gmail.com>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> that's nice to hear this news. If possible, would you please also
> release the input file for simulations since nobody else outside Amber
> developer has any experience for this and there is no documentation yet.
>
> best
> Albert
>
> On 09/14/2012 01:21 PM, Gould, Ian R wrote:
>> Dear All,
>>
>> We have just uploaded our GAFFlipid parameters and other associated
>> files to LipidBook:
>>
>> http://lipidbook.bioch.ox.ac.uk/
>>
>> If you use our parameters please remember to cite our paper.
>>
>> Callum J. Dickson , Lula Rosso , Robin M. Betz , Ross C. Walker and
>> Ian R. Gould, GAFFlipid: a General Amber Force Field for the
>> accurate molecular dynamics simulation of phospholipid, Soft Matter
>> 8 (2012), 9617-9627, doi:
>> 10.1039/C2SM26007G<http://dx.doi.org/10.1039/C2SM26007G>
>>
>> They will also be available from the amber parameter database
>> maintained by Richard Bryce at Manchester in due course.
>>
>> Cheers
>> Ian
>>
>> Women love us for our defects. If we have enough of them, they will
>> forgive us everything, even our intellects.
>> Oscar Wilde,
>> --
>> Dr Ian R Gould
>> Reader in Computational Chemical Biology
>> Department of Chemistry
>> Imperial College London
>> Exhibition Road
>> London
>> SW7 2AY
>> E-mail i.gould.imperial.ac.uk
>> http://www3.imperial.ac.uk/people/i.gould
>> Tel +44 (0)207 594 5809
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 11
> Date: Fri, 14 Sep 2012 21:05:46 +0800 (SGT)
> From: Revthi Sanker <revthi.sanker.yahoo.com>
> Subject: [AMBER] query antechamber-reg
> To: amber.ambermd.org
> Message-ID:
> <1347627946.75319.YahooMailClassic.web193602.mail.sg3.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Dear amber users,
> I am facing problems in using the antechamber utility in amber. I
> have done charge calculation using gaussian and trying to generate
> the prepi file with my gaussian output. Unfortunately, antechamber
> is not able to read the charge from the gaussian output file.I have
> used the following antechamber command -
> ?
> antechamber -i gaussian.log -fi gout -o gaussian.prepin -fo prepi -c esp
>
> Awaiting your valuable comments
>
> Thanks in advance.
> Revthi
>
>
> ------------------------------
>
> Message: 12
> Date: Fri, 14 Sep 2012 13:10:54 +0000
> From: "Dickson, Callum" <callum.dickson09.imperial.ac.uk>
> Subject: Re: [AMBER] GAFFLipid Parameters
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <D2B7798199379F4D88293BEBEB4FFE3D3089D927.icexch-m1.ic.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> The standard protocol we used for bilayer simulation is in the
> methods section of both Lula Rosso's paper from 2008 and our recent
> paper. We did a two stage minimisation, followed by heating in NVT
> and further equilibration in NPT. I have put input files for a
> 72DOPC bilayer below (303K). If you are simulating DPPC or POPE then
> just change the temperatures accordingly.
>
>
> 1) 72_min1.in
>
> first stage minimization
> &cntrl
> imin = 1,
> maxcyc = 1000,
> ncyc = 250,
> ntb = 1,
> ntr = 1,
> cut = 10,
> /
> Hold the solute fixed
> 500.0
> RES 1 72
> END
> END
>
> 2) 72_min2.in
>
> second step of minimization
> &cntrl
> imin = 1,
> maxcyc = 5000,
> ncyc = 2500,
> ntb = 1,
> ntr = 0,
> cut = 10
> /
>
> 3) 72_md1nvt.in
>
> nvt run
> &cntrl
> ig = -1,
> imin = 0,
> nstlim = 10000,
> dt = 0.002,
> irest = 0,
> ntx = 1,
> ntb = 1,
> ntt = 3,
> gamma_ln = 1.0,
> tempi = 0.0,
> temp0 = 303,
> ntr = 1,
> ntc = 2,
> ntf = 2,
> cut = 10,
> ntpr = 100,
> ntwx = 100,
> ntwr = 1000
> /
> Keep solute fixed with weak restraints
> 10.0
> RES 1 72
> END
> END
>
> 4) 72_md2npt.in
>
> npt run
> &cntrl
> imin = 0,
> nstlim = 25000, dt = 0.002,
> irest = 1,
> ntx = 7,
> ntb = 2,
> ntp = 2,
> pres0 = 1.0,
> taup = 0.5,
> ntt = 3, gamma_ln = 1.0, tempi = 303, temp0 = 303,
> ntr = 0,
> ntc = 2, ntf = 2,
> cut = 10,
> ntpr = 100, ntwx = 100, ntwr = 1000
> /
>
> 5) 72_md3npt.in
>
> npt run
> &cntrl
> imin = 0,
> nstlim = 85000, dt = 0.002,
> irest = 1,
> ntx = 7,
> ntb = 2,
> ntp = 2,
> pres0 = 1.0,
> taup = 1.0,
> ntt = 3, gamma_ln = 1.0, tempi = 303, temp0 = 303,
> ntr = 0,
> ntc = 2, ntf = 2,
> cut = 10,
> ntpr = 100, ntwx = 100, ntwr = 1000
> /
>
> 6) 72_npt_50ns_10Acut.in (Example production run of 50ns)
>
> npt production run
> &cntrl
> imin = 0,
> nstlim = 25000000, dt = 0.002,
> irest = 1,
> ntx = 7,
> ntb = 2,
> ntp = 2,
> pres0 = 1.0,
> taup = 1.0,
> ntt = 3, gamma_ln = 1.0, tempi = 303.0, temp0 = 303.0,
> ntr = 0,
> ntc = 2, ntf = 2,
> cut = 10,
> ntpr = 5000, ntwx = 5000, ntwr = 50000
> /
>
>
> Cheers,
> Callum
>
> PhD Student
> Institute of Chemical Biology
> Imperial College London
>
> ________________________________________
> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on
> behalf of Albert [mailmd2011.gmail.com]
> Sent: 14 September 2012 13:39
> To: AMBER Mailing List
> Subject: Re: [AMBER] GAFFLipid Parameters
>
> that's nice to hear this news. If possible, would you please also
> release the input file for simulations since nobody else outside Amber
> developer has any experience for this and there is no documentation yet.
>
> best
> Albert
>
> On 09/14/2012 01:21 PM, Gould, Ian R wrote:
>> Dear All,
>>
>> We have just uploaded our GAFFlipid parameters and other associated
>> files to LipidBook:
>>
>> http://lipidbook.bioch.ox.ac.uk/
>>
>> If you use our parameters please remember to cite our paper.
>>
>> Callum J. Dickson , Lula Rosso , Robin M. Betz , Ross C. Walker and
>> Ian R. Gould, GAFFlipid: a General Amber Force Field for the
>> accurate molecular dynamics simulation of phospholipid, Soft Matter
>> 8 (2012), 9617-9627, doi:
>> 10.1039/C2SM26007G<http://dx.doi.org/10.1039/C2SM26007G>
>>
>> They will also be available from the amber parameter database
>> maintained by Richard Bryce at Manchester in due course.
>>
>> Cheers
>> Ian
>>
>> Women love us for our defects. If we have enough of them, they will
>> forgive us everything, even our intellects.
>> Oscar Wilde,
>> --
>> Dr Ian R Gould
>> Reader in Computational Chemical Biology
>> Department of Chemistry
>> Imperial College London
>> Exhibition Road
>> London
>> SW7 2AY
>> E-mail i.gould.imperial.ac.uk
>> http://www3.imperial.ac.uk/people/i.gould
>> Tel +44 (0)207 594 5809
>> _______________________________________________
>> 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: Fri, 14 Sep 2012 15:29:37 +0200
> From: Albert <mailmd2011.gmail.com>
> Subject: Re: [AMBER] GAFFLipid Parameters
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <50533141.1020603.gmail.com>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> hello Ian:
>
> thank you for such generous comments. May I ask was it finished with
> CPU or GPU? and How fast is it?
>
> thank you very much
> Albert
>
> On 09/14/2012 03:10 PM, Dickson, Callum wrote:
>> The standard protocol we used for bilayer simulation is in the
>> methods section of both Lula Rosso's paper from 2008 and our recent
>> paper. We did a two stage minimisation, followed by heating in NVT
>> and further equilibration in NPT. I have put input files for a
>> 72DOPC bilayer below (303K). If you are simulating DPPC or POPE
>> then just change the temperatures accordingly.
>>
>>
>> 1) 72_min1.in
>>
>> first stage minimization
>> &cntrl
>> imin = 1,
>> maxcyc = 1000,
>> ncyc = 250,
>> ntb = 1,
>> ntr = 1,
>> cut = 10,
>> /
>> Hold the solute fixed
>> 500.0
>> RES 1 72
>> END
>> END
>>
>> 2) 72_min2.in
>>
>> second step of minimization
>> &cntrl
>> imin = 1,
>> maxcyc = 5000,
>> ncyc = 2500,
>> ntb = 1,
>> ntr = 0,
>> cut = 10
>> /
>>
>> 3) 72_md1nvt.in
>>
>> nvt run
>> &cntrl
>> ig = -1,
>> imin = 0,
>> nstlim = 10000,
>> dt = 0.002,
>> irest = 0,
>> ntx = 1,
>> ntb = 1,
>> ntt = 3,
>> gamma_ln = 1.0,
>> tempi = 0.0,
>> temp0 = 303,
>> ntr = 1,
>> ntc = 2,
>> ntf = 2,
>> cut = 10,
>> ntpr = 100,
>> ntwx = 100,
>> ntwr = 1000
>> /
>> Keep solute fixed with weak restraints
>> 10.0
>> RES 1 72
>> END
>> END
>>
>> 4) 72_md2npt.in
>>
>> npt run
>> &cntrl
>> imin = 0,
>> nstlim = 25000, dt = 0.002,
>> irest = 1,
>> ntx = 7,
>> ntb = 2,
>> ntp = 2,
>> pres0 = 1.0,
>> taup = 0.5,
>> ntt = 3, gamma_ln = 1.0, tempi = 303, temp0 = 303,
>> ntr = 0,
>> ntc = 2, ntf = 2,
>> cut = 10,
>> ntpr = 100, ntwx = 100, ntwr = 1000
>> /
>>
>> 5) 72_md3npt.in
>>
>> npt run
>> &cntrl
>> imin = 0,
>> nstlim = 85000, dt = 0.002,
>> irest = 1,
>> ntx = 7,
>> ntb = 2,
>> ntp = 2,
>> pres0 = 1.0,
>> taup = 1.0,
>> ntt = 3, gamma_ln = 1.0, tempi = 303, temp0 = 303,
>> ntr = 0,
>> ntc = 2, ntf = 2,
>> cut = 10,
>> ntpr = 100, ntwx = 100, ntwr = 1000
>> /
>>
>> 6) 72_npt_50ns_10Acut.in (Example production run of 50ns)
>>
>> npt production run
>> &cntrl
>> imin = 0,
>> nstlim = 25000000, dt = 0.002,
>> irest = 1,
>> ntx = 7,
>> ntb = 2,
>> ntp = 2,
>> pres0 = 1.0,
>> taup = 1.0,
>> ntt = 3, gamma_ln = 1.0, tempi = 303.0, temp0 = 303.0,
>> ntr = 0,
>> ntc = 2, ntf = 2,
>> cut = 10,
>> ntpr = 5000, ntwx = 5000, ntwr = 50000
>> /
>>
>>
>> Cheers,
>> Callum
>>
>> PhD Student
>> Institute of Chemical Biology
>> Imperial College London
>>
>> ________________________________________
>> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on
>> behalf of Albert [mailmd2011.gmail.com]
>> Sent: 14 September 2012 13:39
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] GAFFLipid Parameters
>>
>> that's nice to hear this news. If possible, would you please also
>> release the input file for simulations since nobody else outside Amber
>> developer has any experience for this and there is no documentation yet.
>>
>> best
>> Albert
>>
>> On 09/14/2012 01:21 PM, Gould, Ian R wrote:
>>> Dear All,
>>>
>>> We have just uploaded our GAFFlipid parameters and other
>>> associated files to LipidBook:
>>>
>>> http://lipidbook.bioch.ox.ac.uk/
>>>
>>> If you use our parameters please remember to cite our paper.
>>>
>>> Callum J. Dickson , Lula Rosso , Robin M. Betz , Ross C. Walker
>>> and Ian R. Gould, GAFFlipid: a General Amber Force Field for the
>>> accurate molecular dynamics simulation of phospholipid, Soft
>>> Matter 8 (2012), 9617-9627, doi:
>>> 10.1039/C2SM26007G<http://dx.doi.org/10.1039/C2SM26007G>
>>>
>>> They will also be available from the amber parameter database
>>> maintained by Richard Bryce at Manchester in due course.
>>>
>>> Cheers
>>> Ian
>>>
>>> Women love us for our defects. If we have enough of them, they
>>> will forgive us everything, even our intellects.
>>> Oscar Wilde,
>>> --
>>> Dr Ian R Gould
>>> Reader in Computational Chemical Biology
>>> Department of Chemistry
>>> Imperial College London
>>> Exhibition Road
>>> London
>>> SW7 2AY
>>> E-mail i.gould.imperial.ac.uk
>>> http://www3.imperial.ac.uk/people/i.gould
>>> Tel +44 (0)207 594 5809
>>> _______________________________________________
>>> 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: Fri, 14 Sep 2012 13:36:35 +0000
> From: "Dickson, Callum" <callum.dickson09.imperial.ac.uk>
> Subject: Re: [AMBER] GAFFLipid Parameters
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <D2B7798199379F4D88293BEBEB4FFE3D3089D93B.icexch-m1.ic.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> All of our runs were on GPUs with the amber11 cuda code, generally
> achieving around 30ns/day for a 72 lipid bilayer (the 288 bilayers
> were around 7ns/day).
>
> Best,
> Callum
> ________________________________________
> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on
> behalf of Albert [mailmd2011.gmail.com]
> Sent: 14 September 2012 14:29
> To: AMBER Mailing List
> Subject: Re: [AMBER] GAFFLipid Parameters
>
> hello Ian:
>
> thank you for such generous comments. May I ask was it finished with
> CPU or GPU? and How fast is it?
>
> thank you very much
> Albert
>
> On 09/14/2012 03:10 PM, Dickson, Callum wrote:
>> The standard protocol we used for bilayer simulation is in the
>> methods section of both Lula Rosso's paper from 2008 and our recent
>> paper. We did a two stage minimisation, followed by heating in NVT
>> and further equilibration in NPT. I have put input files for a
>> 72DOPC bilayer below (303K). If you are simulating DPPC or POPE
>> then just change the temperatures accordingly.
>>
>>
>> 1) 72_min1.in
>>
>> first stage minimization
>> &cntrl
>> imin = 1,
>> maxcyc = 1000,
>> ncyc = 250,
>> ntb = 1,
>> ntr = 1,
>> cut = 10,
>> /
>> Hold the solute fixed
>> 500.0
>> RES 1 72
>> END
>> END
>>
>> 2) 72_min2.in
>>
>> second step of minimization
>> &cntrl
>> imin = 1,
>> maxcyc = 5000,
>> ncyc = 2500,
>> ntb = 1,
>> ntr = 0,
>> cut = 10
>> /
>>
>> 3) 72_md1nvt.in
>>
>> nvt run
>> &cntrl
>> ig = -1,
>> imin = 0,
>> nstlim = 10000,
>> dt = 0.002,
>> irest = 0,
>> ntx = 1,
>> ntb = 1,
>> ntt = 3,
>> gamma_ln = 1.0,
>> tempi = 0.0,
>> temp0 = 303,
>> ntr = 1,
>> ntc = 2,
>> ntf = 2,
>> cut = 10,
>> ntpr = 100,
>> ntwx = 100,
>> ntwr = 1000
>> /
>> Keep solute fixed with weak restraints
>> 10.0
>> RES 1 72
>> END
>> END
>>
>> 4) 72_md2npt.in
>>
>> npt run
>> &cntrl
>> imin = 0,
>> nstlim = 25000, dt = 0.002,
>> irest = 1,
>> ntx = 7,
>> ntb = 2,
>> ntp = 2,
>> pres0 = 1.0,
>> taup = 0.5,
>> ntt = 3, gamma_ln = 1.0, tempi = 303, temp0 = 303,
>> ntr = 0,
>> ntc = 2, ntf = 2,
>> cut = 10,
>> ntpr = 100, ntwx = 100, ntwr = 1000
>> /
>>
>> 5) 72_md3npt.in
>>
>> npt run
>> &cntrl
>> imin = 0,
>> nstlim = 85000, dt = 0.002,
>> irest = 1,
>> ntx = 7,
>> ntb = 2,
>> ntp = 2,
>> pres0 = 1.0,
>> taup = 1.0,
>> ntt = 3, gamma_ln = 1.0, tempi = 303, temp0 = 303,
>> ntr = 0,
>> ntc = 2, ntf = 2,
>> cut = 10,
>> ntpr = 100, ntwx = 100, ntwr = 1000
>> /
>>
>> 6) 72_npt_50ns_10Acut.in (Example production run of 50ns)
>>
>> npt production run
>> &cntrl
>> imin = 0,
>> nstlim = 25000000, dt = 0.002,
>> irest = 1,
>> ntx = 7,
>> ntb = 2,
>> ntp = 2,
>> pres0 = 1.0,
>> taup = 1.0,
>> ntt = 3, gamma_ln = 1.0, tempi = 303.0, temp0 = 303.0,
>> ntr = 0,
>> ntc = 2, ntf = 2,
>> cut = 10,
>> ntpr = 5000, ntwx = 5000, ntwr = 50000
>> /
>>
>>
>> Cheers,
>> Callum
>>
>> PhD Student
>> Institute of Chemical Biology
>> Imperial College London
>>
>> ________________________________________
>> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on
>> behalf of Albert [mailmd2011.gmail.com]
>> Sent: 14 September 2012 13:39
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] GAFFLipid Parameters
>>
>> that's nice to hear this news. If possible, would you please also
>> release the input file for simulations since nobody else outside Amber
>> developer has any experience for this and there is no documentation yet.
>>
>> best
>> Albert
>>
>> On 09/14/2012 01:21 PM, Gould, Ian R wrote:
>>> Dear All,
>>>
>>> We have just uploaded our GAFFlipid parameters and other
>>> associated files to LipidBook:
>>>
>>> http://lipidbook.bioch.ox.ac.uk/
>>>
>>> If you use our parameters please remember to cite our paper.
>>>
>>> Callum J. Dickson , Lula Rosso , Robin M. Betz , Ross C. Walker
>>> and Ian R. Gould, GAFFlipid: a General Amber Force Field for the
>>> accurate molecular dynamics simulation of phospholipid, Soft
>>> Matter 8 (2012), 9617-9627, doi:
>>> 10.1039/C2SM26007G<http://dx.doi.org/10.1039/C2SM26007G>
>>>
>>> They will also be available from the amber parameter database
>>> maintained by Richard Bryce at Manchester in due course.
>>>
>>> Cheers
>>> Ian
>>>
>>> Women love us for our defects. If we have enough of them, they
>>> will forgive us everything, even our intellects.
>>> Oscar Wilde,
>>> --
>>> Dr Ian R Gould
>>> Reader in Computational Chemical Biology
>>> Department of Chemistry
>>> Imperial College London
>>> Exhibition Road
>>> London
>>> SW7 2AY
>>> E-mail i.gould.imperial.ac.uk
>>> http://www3.imperial.ac.uk/people/i.gould
>>> Tel +44 (0)207 594 5809
>>> _______________________________________________
>>> 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: Fri, 14 Sep 2012 09:39:11 -0400
> From: Adrian Roitberg <roitberg.ufl.edu>
> Subject: Re: [AMBER] GAFFLipid Parameters
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <5053337F.6080404.ufl.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Callum:
>
> did you get away with it without needing a surface tension term? That
> would be awesome !
>
> adrian
>
>
> On 9/14/12 9:36 AM, Dickson, Callum wrote:
>> Hi,
>>
>> All of our runs were on GPUs with the amber11 cuda code, generally
>> achieving around 30ns/day for a 72 lipid bilayer (the 288 bilayers
>> were around 7ns/day).
>>
>> Best,
>> Callum
>> ________________________________________
>> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on
>> behalf of Albert [mailmd2011.gmail.com]
>> Sent: 14 September 2012 14:29
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] GAFFLipid Parameters
>>
>> hello Ian:
>>
>> thank you for such generous comments. May I ask was it finished with
>> CPU or GPU? and How fast is it?
>>
>> thank you very much
>> Albert
>>
>> On 09/14/2012 03:10 PM, Dickson, Callum wrote:
>>> The standard protocol we used for bilayer simulation is in the
>>> methods section of both Lula Rosso's paper from 2008 and our
>>> recent paper. We did a two stage minimisation, followed by heating
>>> in NVT and further equilibration in NPT. I have put input files
>>> for a 72DOPC bilayer below (303K). If you are simulating DPPC or
>>> POPE then just change the temperatures accordingly.
>>>
>>>
>>> 1) 72_min1.in
>>>
>>> first stage minimization
>>> &cntrl
>>> imin = 1,
>>> maxcyc = 1000,
>>> ncyc = 250,
>>> ntb = 1,
>>> ntr = 1,
>>> cut = 10,
>>> /
>>> Hold the solute fixed
>>> 500.0
>>> RES 1 72
>>> END
>>> END
>>>
>>> 2) 72_min2.in
>>>
>>> second step of minimization
>>> &cntrl
>>> imin = 1,
>>> maxcyc = 5000,
>>> ncyc = 2500,
>>> ntb = 1,
>>> ntr = 0,
>>> cut = 10
>>> /
>>>
>>> 3) 72_md1nvt.in
>>>
>>> nvt run
>>> &cntrl
>>> ig = -1,
>>> imin = 0,
>>> nstlim = 10000,
>>> dt = 0.002,
>>> irest = 0,
>>> ntx = 1,
>>> ntb = 1,
>>> ntt = 3,
>>> gamma_ln = 1.0,
>>> tempi = 0.0,
>>> temp0 = 303,
>>> ntr = 1,
>>> ntc = 2,
>>> ntf = 2,
>>> cut = 10,
>>> ntpr = 100,
>>> ntwx = 100,
>>> ntwr = 1000
>>> /
>>> Keep solute fixed with weak restraints
>>> 10.0
>>> RES 1 72
>>> END
>>> END
>>>
>>> 4) 72_md2npt.in
>>>
>>> npt run
>>> &cntrl
>>> imin = 0,
>>> nstlim = 25000, dt = 0.002,
>>> irest = 1,
>>> ntx = 7,
>>> ntb = 2,
>>> ntp = 2,
>>> pres0 = 1.0,
>>> taup = 0.5,
>>> ntt = 3, gamma_ln = 1.0, tempi = 303, temp0 = 303,
>>> ntr = 0,
>>> ntc = 2, ntf = 2,
>>> cut = 10,
>>> ntpr = 100, ntwx = 100, ntwr = 1000
>>> /
>>>
>>> 5) 72_md3npt.in
>>>
>>> npt run
>>> &cntrl
>>> imin = 0,
>>> nstlim = 85000, dt = 0.002,
>>> irest = 1,
>>> ntx = 7,
>>> ntb = 2,
>>> ntp = 2,
>>> pres0 = 1.0,
>>> taup = 1.0,
>>> ntt = 3, gamma_ln = 1.0, tempi = 303, temp0 = 303,
>>> ntr = 0,
>>> ntc = 2, ntf = 2,
>>> cut = 10,
>>> ntpr = 100, ntwx = 100, ntwr = 1000
>>> /
>>>
>>> 6) 72_npt_50ns_10Acut.in (Example production run of 50ns)
>>>
>>> npt production run
>>> &cntrl
>>> imin = 0,
>>> nstlim = 25000000, dt = 0.002,
>>> irest = 1,
>>> ntx = 7,
>>> ntb = 2,
>>> ntp = 2,
>>> pres0 = 1.0,
>>> taup = 1.0,
>>> ntt = 3, gamma_ln = 1.0, tempi = 303.0, temp0 = 303.0,
>>> ntr = 0,
>>> ntc = 2, ntf = 2,
>>> cut = 10,
>>> ntpr = 5000, ntwx = 5000, ntwr = 50000
>>> /
>>>
>>>
>>> Cheers,
>>> Callum
>>>
>>> PhD Student
>>> Institute of Chemical Biology
>>> Imperial College London
>>>
>>> ________________________________________
>>> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on
>>> behalf of Albert [mailmd2011.gmail.com]
>>> Sent: 14 September 2012 13:39
>>> To: AMBER Mailing List
>>> Subject: Re: [AMBER] GAFFLipid Parameters
>>>
>>> that's nice to hear this news. If possible, would you please also
>>> release the input file for simulations since nobody else outside Amber
>>> developer has any experience for this and there is no documentation yet.
>>>
>>> best
>>> Albert
>>>
>>> On 09/14/2012 01:21 PM, Gould, Ian R wrote:
>>>> Dear All,
>>>>
>>>> We have just uploaded our GAFFlipid parameters and other
>>>> associated files to LipidBook:
>>>>
>>>> http://lipidbook.bioch.ox.ac.uk/
>>>>
>>>> If you use our parameters please remember to cite our paper.
>>>>
>>>> Callum J. Dickson , Lula Rosso , Robin M. Betz , Ross C. Walker
>>>> and Ian R. Gould, GAFFlipid: a General Amber Force Field for the
>>>> accurate molecular dynamics simulation of phospholipid, Soft
>>>> Matter 8 (2012), 9617-9627, doi:
>>>> 10.1039/C2SM26007G<http://dx.doi.org/10.1039/C2SM26007G>
>>>>
>>>> They will also be available from the amber parameter database
>>>> maintained by Richard Bryce at Manchester in due course.
>>>>
>>>> Cheers
>>>> Ian
>>>>
>>>> Women love us for our defects. If we have enough of them, they
>>>> will forgive us everything, even our intellects.
>>>> Oscar Wilde,
>>>> --
>>>> Dr Ian R Gould
>>>> Reader in Computational Chemical Biology
>>>> Department of Chemistry
>>>> Imperial College London
>>>> Exhibition Road
>>>> London
>>>> SW7 2AY
>>>> E-mail i.gould.imperial.ac.uk
>>>> http://www3.imperial.ac.uk/people/i.gould
>>>> Tel +44 (0)207 594 5809
>>>> _______________________________________________
>>>> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> --
> Dr. Adrian E. Roitberg
> Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
>
>
>
> ------------------------------
>
> Message: 16
> Date: Fri, 14 Sep 2012 13:44:57 +0000
> From: "Dickson, Callum" <callum.dickson09.imperial.ac.uk>
> Subject: Re: [AMBER] GAFFLipid Parameters
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <D2B7798199379F4D88293BEBEB4FFE3D3089D94E.icexch-m1.ic.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Adrian,
>
> There was no surface tension applied, that was essentially the point
> of this work if you have a look at the paper! The van der Waals
> parameters of the lipid carbon chains needed correcting to avoid the
> use of a surface tension.
> We will be incorporating these parameters with lipid11 soon.
>
> Cheers,
> Callum
> ________________________________________
> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on
> behalf of Adrian Roitberg [roitberg.ufl.edu]
> Sent: 14 September 2012 14:39
> To: AMBER Mailing List
> Subject: Re: [AMBER] GAFFLipid Parameters
>
> Callum:
>
> did you get away with it without needing a surface tension term? That
> would be awesome !
>
> adrian
>
>
> On 9/14/12 9:36 AM, Dickson, Callum wrote:
>> Hi,
>>
>> All of our runs were on GPUs with the amber11 cuda code, generally
>> achieving around 30ns/day for a 72 lipid bilayer (the 288 bilayers
>> were around 7ns/day).
>>
>> Best,
>> Callum
>> ________________________________________
>> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on
>> behalf of Albert [mailmd2011.gmail.com]
>> Sent: 14 September 2012 14:29
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] GAFFLipid Parameters
>>
>> hello Ian:
>>
>> thank you for such generous comments. May I ask was it finished with
>> CPU or GPU? and How fast is it?
>>
>> thank you very much
>> Albert
>>
>> On 09/14/2012 03:10 PM, Dickson, Callum wrote:
>>> The standard protocol we used for bilayer simulation is in the
>>> methods section of both Lula Rosso's paper from 2008 and our
>>> recent paper. We did a two stage minimisation, followed by heating
>>> in NVT and further equilibration in NPT. I have put input files
>>> for a 72DOPC bilayer below (303K). If you are simulating DPPC or
>>> POPE then just change the temperatures accordingly.
>>>
>>>
>>> 1) 72_min1.in
>>>
>>> first stage minimization
>>> &cntrl
>>> imin = 1,
>>> maxcyc = 1000,
>>> ncyc = 250,
>>> ntb = 1,
>>> ntr = 1,
>>> cut = 10,
>>> /
>>> Hold the solute fixed
>>> 500.0
>>> RES 1 72
>>> END
>>> END
>>>
>>> 2) 72_min2.in
>>>
>>> second step of minimization
>>> &cntrl
>>> imin = 1,
>>> maxcyc = 5000,
>>> ncyc = 2500,
>>> ntb = 1,
>>> ntr = 0,
>>> cut = 10
>>> /
>>>
>>> 3) 72_md1nvt.in
>>>
>>> nvt run
>>> &cntrl
>>> ig = -1,
>>> imin = 0,
>>> nstlim = 10000,
>>> dt = 0.002,
>>> irest = 0,
>>> ntx = 1,
>>> ntb = 1,
>>> ntt = 3,
>>> gamma_ln = 1.0,
>>> tempi = 0.0,
>>> temp0 = 303,
>>> ntr = 1,
>>> ntc = 2,
>>> ntf = 2,
>>> cut = 10,
>>> ntpr = 100,
>>> ntwx = 100,
>>> ntwr = 1000
>>> /
>>> Keep solute fixed with weak restraints
>>> 10.0
>>> RES 1 72
>>> END
>>> END
>>>
>>> 4) 72_md2npt.in
>>>
>>> npt run
>>> &cntrl
>>> imin = 0,
>>> nstlim = 25000, dt = 0.002,
>>> irest = 1,
>>> ntx = 7,
>>> ntb = 2,
>>> ntp = 2,
>>> pres0 = 1.0,
>>> taup = 0.5,
>>> ntt = 3, gamma_ln = 1.0, tempi = 303, temp0 = 303,
>>> ntr = 0,
>>> ntc = 2, ntf = 2,
>>> cut = 10,
>>> ntpr = 100, ntwx = 100, ntwr = 1000
>>> /
>>>
>>> 5) 72_md3npt.in
>>>
>>> npt run
>>> &cntrl
>>> imin = 0,
>>> nstlim = 85000, dt = 0.002,
>>> irest = 1,
>>> ntx = 7,
>>> ntb = 2,
>>> ntp = 2,
>>> pres0 = 1.0,
>>> taup = 1.0,
>>> ntt = 3, gamma_ln = 1.0, tempi = 303, temp0 = 303,
>>> ntr = 0,
>>> ntc = 2, ntf = 2,
>>> cut = 10,
>>> ntpr = 100, ntwx = 100, ntwr = 1000
>>> /
>>>
>>> 6) 72_npt_50ns_10Acut.in (Example production run of 50ns)
>>>
>>> npt production run
>>> &cntrl
>>> imin = 0,
>>> nstlim = 25000000, dt = 0.002,
>>> irest = 1,
>>> ntx = 7,
>>> ntb = 2,
>>> ntp = 2,
>>> pres0 = 1.0,
>>> taup = 1.0,
>>> ntt = 3, gamma_ln = 1.0, tempi = 303.0, temp0 = 303.0,
>>> ntr = 0,
>>> ntc = 2, ntf = 2,
>>> cut = 10,
>>> ntpr = 5000, ntwx = 5000, ntwr = 50000
>>> /
>>>
>>>
>>> Cheers,
>>> Callum
>>>
>>> PhD Student
>>> Institute of Chemical Biology
>>> Imperial College London
>>>
>>> ________________________________________
>>> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on
>>> behalf of Albert [mailmd2011.gmail.com]
>>> Sent: 14 September 2012 13:39
>>> To: AMBER Mailing List
>>> Subject: Re: [AMBER] GAFFLipid Parameters
>>>
>>> that's nice to hear this news. If possible, would you please also
>>> release the input file for simulations since nobody else outside Amber
>>> developer has any experience for this and there is no documentation yet.
>>>
>>> best
>>> Albert
>>>
>>> On 09/14/2012 01:21 PM, Gould, Ian R wrote:
>>>> Dear All,
>>>>
>>>> We have just uploaded our GAFFlipid parameters and other
>>>> associated files to LipidBook:
>>>>
>>>> http://lipidbook.bioch.ox.ac.uk/
>>>>
>>>> If you use our parameters please remember to cite our paper.
>>>>
>>>> Callum J. Dickson , Lula Rosso , Robin M. Betz , Ross C. Walker
>>>> and Ian R. Gould, GAFFlipid: a General Amber Force Field for the
>>>> accurate molecular dynamics simulation of phospholipid, Soft
>>>> Matter 8 (2012), 9617-9627, doi:
>>>> 10.1039/C2SM26007G<http://dx.doi.org/10.1039/C2SM26007G>
>>>>
>>>> They will also be available from the amber parameter database
>>>> maintained by Richard Bryce at Manchester in due course.
>>>>
>>>> Cheers
>>>> Ian
>>>>
>>>> Women love us for our defects. If we have enough of them, they
>>>> will forgive us everything, even our intellects.
>>>> Oscar Wilde,
>>>> --
>>>> Dr Ian R Gould
>>>> Reader in Computational Chemical Biology
>>>> Department of Chemistry
>>>> Imperial College London
>>>> Exhibition Road
>>>> London
>>>> SW7 2AY
>>>> E-mail i.gould.imperial.ac.uk
>>>> http://www3.imperial.ac.uk/people/i.gould
>>>> Tel +44 (0)207 594 5809
>>>> _______________________________________________
>>>> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> --
> Dr. Adrian E. Roitberg
> Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 17
> Date: Fri, 14 Sep 2012 09:48:51 -0400
> From: Adrian Roitberg <roitberg.ufl.edu>
> Subject: Re: [AMBER] GAFFLipid Parameters
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <505335C3.9080102.ufl.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Right, I agree, this was the missing link! I will read the paper, but it
> looks like you guys pulled it off. Finally we should be able to simulate
> lipids without having to break simple laws of physics like everyone else
> has been doing.
>
> I gave up on lipid simulations a long time ago after checking that the
> results were simply not believable.
>
> adrian
>
>
> On 9/14/12 9:44 AM, Dickson, Callum wrote:
>> Hi Adrian,
>>
>> There was no surface tension applied, that was essentially the
>> point of this work if you have a look at the paper! The van der
>> Waals parameters of the lipid carbon chains needed correcting to
>> avoid the use of a surface tension.
>> We will be incorporating these parameters with lipid11 soon.
>>
>> Cheers,
>> Callum
>> ________________________________________
>> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on
>> behalf of Adrian Roitberg [roitberg.ufl.edu]
>> Sent: 14 September 2012 14:39
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] GAFFLipid Parameters
>>
>> Callum:
>>
>> did you get away with it without needing a surface tension term? That
>> would be awesome !
>>
>> adrian
>>
>>
>> On 9/14/12 9:36 AM, Dickson, Callum wrote:
>>> Hi,
>>>
>>> All of our runs were on GPUs with the amber11 cuda code, generally
>>> achieving around 30ns/day for a 72 lipid bilayer (the 288 bilayers
>>> were around 7ns/day).
>>>
>>> Best,
>>> Callum
>>> ________________________________________
>>> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on
>>> behalf of Albert [mailmd2011.gmail.com]
>>> Sent: 14 September 2012 14:29
>>> To: AMBER Mailing List
>>> Subject: Re: [AMBER] GAFFLipid Parameters
>>>
>>> hello Ian:
>>>
>>> thank you for such generous comments. May I ask was it finished with
>>> CPU or GPU? and How fast is it?
>>>
>>> thank you very much
>>> Albert
>>>
>>> On 09/14/2012 03:10 PM, Dickson, Callum wrote:
>>>> The standard protocol we used for bilayer simulation is in the
>>>> methods section of both Lula Rosso's paper from 2008 and our
>>>> recent paper. We did a two stage minimisation, followed by
>>>> heating in NVT and further equilibration in NPT. I have put input
>>>> files for a 72DOPC bilayer below (303K). If you are simulating
>>>> DPPC or POPE then just change the temperatures accordingly.
>>>>
>>>>
>>>> 1) 72_min1.in
>>>>
>>>> first stage minimization
>>>> &cntrl
>>>> imin = 1,
>>>> maxcyc = 1000,
>>>> ncyc = 250,
>>>> ntb = 1,
>>>> ntr = 1,
>>>> cut = 10,
>>>> /
>>>> Hold the solute fixed
>>>> 500.0
>>>> RES 1 72
>>>> END
>>>> END
>>>>
>>>> 2) 72_min2.in
>>>>
>>>> second step of minimization
>>>> &cntrl
>>>> imin = 1,
>>>> maxcyc = 5000,
>>>> ncyc = 2500,
>>>> ntb = 1,
>>>> ntr = 0,
>>>> cut = 10
>>>> /
>>>>
>>>> 3) 72_md1nvt.in
>>>>
>>>> nvt run
>>>> &cntrl
>>>> ig = -1,
>>>> imin = 0,
>>>> nstlim = 10000,
>>>> dt = 0.002,
>>>> irest = 0,
>>>> ntx = 1,
>>>> ntb = 1,
>>>> ntt = 3,
>>>> gamma_ln = 1.0,
>>>> tempi = 0.0,
>>>> temp0 = 303,
>>>> ntr = 1,
>>>> ntc = 2,
>>>> ntf = 2,
>>>> cut = 10,
>>>> ntpr = 100,
>>>> ntwx = 100,
>>>> ntwr = 1000
>>>> /
>>>> Keep solute fixed with weak restraints
>>>> 10.0
>>>> RES 1 72
>>>> END
>>>> END
>>>>
>>>> 4) 72_md2npt.in
>>>>
>>>> npt run
>>>> &cntrl
>>>> imin = 0,
>>>> nstlim = 25000, dt = 0.002,
>>>> irest = 1,
>>>> ntx = 7,
>>>> ntb = 2,
>>>> ntp = 2,
>>>> pres0 = 1.0,
>>>> taup = 0.5,
>>>> ntt = 3, gamma_ln = 1.0, tempi = 303, temp0 = 303,
>>>> ntr = 0,
>>>> ntc = 2, ntf = 2,
>>>> cut = 10,
>>>> ntpr = 100, ntwx = 100, ntwr = 1000
>>>> /
>>>>
>>>> 5) 72_md3npt.in
>>>>
>>>> npt run
>>>> &cntrl
>>>> imin = 0,
>>>> nstlim = 85000, dt = 0.002,
>>>> irest = 1,
>>>> ntx = 7,
>>>> ntb = 2,
>>>> ntp = 2,
>>>> pres0 = 1.0,
>>>> taup = 1.0,
>>>> ntt = 3, gamma_ln = 1.0, tempi = 303, temp0 = 303,
>>>> ntr = 0,
>>>> ntc = 2, ntf = 2,
>>>> cut = 10,
>>>> ntpr = 100, ntwx = 100, ntwr = 1000
>>>> /
>>>>
>>>> 6) 72_npt_50ns_10Acut.in (Example production run of 50ns)
>>>>
>>>> npt production run
>>>> &cntrl
>>>> imin = 0,
>>>> nstlim = 25000000, dt = 0.002,
>>>> irest = 1,
>>>> ntx = 7,
>>>> ntb = 2,
>>>> ntp = 2,
>>>> pres0 = 1.0,
>>>> taup = 1.0,
>>>> ntt = 3, gamma_ln = 1.0, tempi = 303.0, temp0 = 303.0,
>>>> ntr = 0,
>>>> ntc = 2, ntf = 2,
>>>> cut = 10,
>>>> ntpr = 5000, ntwx = 5000, ntwr = 50000
>>>> /
>>>>
>>>>
>>>> Cheers,
>>>> Callum
>>>>
>>>> PhD Student
>>>> Institute of Chemical Biology
>>>> Imperial College London
>>>>
>>>> ________________________________________
>>>> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on
>>>> behalf of Albert [mailmd2011.gmail.com]
>>>> Sent: 14 September 2012 13:39
>>>> To: AMBER Mailing List
>>>> Subject: Re: [AMBER] GAFFLipid Parameters
>>>>
>>>> that's nice to hear this news. If possible, would you please also
>>>> release the input file for simulations since nobody else outside Amber
>>>> developer has any experience for this and there is no documentation yet.
>>>>
>>>> best
>>>> Albert
>>>>
>>>> On 09/14/2012 01:21 PM, Gould, Ian R wrote:
>>>>> Dear All,
>>>>>
>>>>> We have just uploaded our GAFFlipid parameters and other
>>>>> associated files to LipidBook:
>>>>>
>>>>> http://lipidbook.bioch.ox.ac.uk/
>>>>>
>>>>> If you use our parameters please remember to cite our paper.
>>>>>
>>>>> Callum J. Dickson , Lula Rosso , Robin M. Betz , Ross C. Walker
>>>>> and Ian R. Gould, GAFFlipid: a General Amber Force Field for the
>>>>> accurate molecular dynamics simulation of phospholipid, Soft
>>>>> Matter 8 (2012), 9617-9627, doi:
>>>>> 10.1039/C2SM26007G<http://dx.doi.org/10.1039/C2SM26007G>
>>>>>
>>>>> They will also be available from the amber parameter database
>>>>> maintained by Richard Bryce at Manchester in due course.
>>>>>
>>>>> Cheers
>>>>> Ian
>>>>>
>>>>> Women love us for our defects. If we have enough of them, they
>>>>> will forgive us everything, even our intellects.
>>>>> Oscar Wilde,
>>>>> --
>>>>> Dr Ian R Gould
>>>>> Reader in Computational Chemical Biology
>>>>> Department of Chemistry
>>>>> Imperial College London
>>>>> Exhibition Road
>>>>> London
>>>>> SW7 2AY
>>>>> E-mail i.gould.imperial.ac.uk
>>>>> http://www3.imperial.ac.uk/people/i.gould
>>>>> Tel +44 (0)207 594 5809
>>>>> _______________________________________________
>>>>> 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
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>> --
>> Dr. Adrian E. Roitberg
>> Professor
>> Quantum Theory Project, Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>>
>> _______________________________________________
>> 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
>>
>
> --
> Dr. Adrian E. Roitberg
> Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
>
>
>
> ------------------------------
>
> Message: 18
> Date: Fri, 14 Sep 2012 09:58:15 -0400
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] query antechamber-reg
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20120914135815.GC77794.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=iso-8859-1
>
> On Fri, Sep 14, 2012, Revthi Sanker wrote:
>
>> I am facing problems in using the antechamber utility in amber. I have
>> done charge calculation using gaussian and trying to generate the prepi
>> file with my gaussian output. Unfortunately, antechamber is not able to
>> read the charge from the gaussian output file.I have used the following
>> antechamber command -
>> ?
>> antechamber -i gaussian.log -fi gout -o gaussian.prepin -fo prepi -c esp
>
> I don't think anyone can help without seeing your input file.
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 19
> Date: Fri, 14 Sep 2012 09:59:50 -0400
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] Error in converstion of pdb to mol2
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20120914135950.GD77794.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Fri, Sep 14, 2012, Anogna wrote:
>>
>> The following is my ligand pdb file
>>
>> HETATM 8833 C1 COM A 1 19.831 16.769 69.471 1.00 0.00
>> HETATM 8834 C2 COM A 1 20.941 17.638 69.469 1.00 0.00
>> HETATM 8835 C3 COM A 1 19.620 15.877 68.404 1.00 0.00
>> HETATM 8836 C4 COM A 1 21.863 17.622 68.383 1.00 0.00
>> HETATM 8837 C5 COM A 1 20.523 15.850 67.326 1.00 0.00
>> HETATM 8838 C6 COM A 1 21.633 16.717 67.318 1.00 0.00
>> HETATM 8839 C7 COM A 1 23.070 18.532 68.329 1.00 0.00
>> HETATM 8840 O8 COM A 1 24.030 18.214 67.593 1.00 0.00
>> HETATM 8841 O9 COM A 1 21.089 18.480 70.534 1.00 0.00
>> HETATM 8842 N10 COM A 1 20.326 15.002 66.307 1.00 0.00
>> HETATM 8843 O17 COM A 1 23.087 19.579 69.016 1.00 0.00
>
> You don't have any hydrogens! Those are required to use antechamber.
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 20
> Date: Fri, 14 Sep 2012 10:05:00 -0400
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] POL3 water model run error...
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20120914140500.GE77794.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=utf-8
>
> On Tue, Sep 11, 2012, ?? ? wrote:
>
>> Recently, I was running the POL3 bulk water using amber11, though i
>> can pass the minimization, when i run the NVT simulation, something
>> strange happened..
>
> You might try looking at the files in amber12/test/test_leap_ff11. These are
> not run by default, but the "RUN" and "RUN.ARD" scripts there test pol3. You
> might see if those work, and (if so) how they are different from your input
> files.
>
> ...good luck...dac
>
>
>
>
> ------------------------------
>
> Message: 21
> Date: Fri, 14 Sep 2012 16:13:21 +0200
> From: Albert <mailmd2011.gmail.com>
> Subject: Re: [AMBER] GAFFLipid Parameters
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <50533B81.9020206.gmail.com>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> On 09/14/2012 03:36 PM, Dickson, Callum wrote:
>> Hi,
>>
>> All of our runs were on GPUs with the amber11 cuda code, generally
>> achieving around 30ns/day for a 72 lipid bilayer (the 288 bilayers
>> were around 7ns/day).
>>
>> Best,
>> Callum
>> _________________
>
>
> That's since to be nice. Does anybody also consider improve the CPU
> performance of Amber? I can only get max. 10 ns/day for normal 50,000
> protein/water system with cutoff=0.8 while I can easily get upto 30-40
> ns/day with another two MD tools with cutoff 1.0 under Amber99-ILDN FF.
> That's really headache for the CPU poor performance of Amber. Hopefully
> it can also be improved in the near future.
>
> best
> Albert
>
>
>
> ------------------------------
>
> Message: 22
> Date: Fri, 14 Sep 2012 09:01:05 -0700
> From: Ross Walker <ross.rosswalker.co.uk>
> Subject: Re: [AMBER] GAFFLipid Parameters
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <CC78A0E7.E228%ross.rosswalker.co.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> Hi Albert,
>
>> That's since to be nice. Does anybody also consider improve the CPU
>> performance of Amber? I can only get max. 10 ns/day for normal 50,000
>> protein/water system with cutoff=0.8 while I can easily get upto 30-40
>> ns/day with another two MD tools with cutoff 1.0 under Amber99-ILDN FF.
>> That's really headache for the CPU poor performance of Amber. Hopefully
>> it can also be improved in the near future.
>
>
> I suspect you are not doing an apples to apples comparison in terms of CPU
> performance. There is a big (but sometimes subtle, or not well described)
> difference between improving performance and increasing the number of
> approximations used. If you are comparing to Gromacs then for a fair
> comparison you should use the double precision version of the code, only
> shake hydrogen bond lengths, use a 2 fs time step, make sure you are using
> PME with the same grid spacing, ewald coefficient and interpolation order,
> make sure you are doing the PME on every time step and use either NVE or
> the same thermostat if supported in both codes. Otherwise you are not
> comparing the same thing.
>
>
> If you want to compare to NAMD please see the following page which
> explains how to run the AMBER force fields correctly in NAMD:
>
> http://ambermd.org/namd/namd_amber.html
>
> Note the benchmark on that page which is for a reasonably good apples to
> apples comparison. The same caveats apply, use the same level of,
> conservative, approximations in both codes.
>
> Now as to whether one should make extensive approximations to the
> underlying mathematical model in search of greater performance that is a
> very big can of worms and a discussion for another day, ideally over a
> reasonably large number of pints of beer.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 23
> Date: Fri, 14 Sep 2012 16:39:02 +0000
> From: "Shahoei, Seyyedehrezvan" <shahoei2.illinois.edu>
> Subject: Re: [AMBER] Antibiotics Parameters
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID:
> <C939F400AA4B944CB4D59BDA24A272B80C9C4E8C.CITESMBX1.ad.uillinois.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Thanks Francois for your help , I guess I am on the track now. RED
> is a bit time consuming but due to what you said it worths it.
>
> A quick unrelated question: What is the latest antechamber version
> with mopac?
>
> Thank you,
> Rezvan
>
>
> On Sep 8, 2012, at 10:10 AM, FyD wrote:
>
>> Dear Rezvan,
>>
>>> I followed your suggestion and tried R.E.D. I basically don't
>>> understand what is going on in Fig 1 of the tutorials.
>>
>> So we missed the role of this image ;-)
>>
>>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
>>>> or
>>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#1
>>
>> This image tries to summarize the central role of a force field
>> library (or a set of force field libraries in the mol2 (or mol3
>> file format)) when one wishes to run MD simulations at
>> q4md-forcefieldtools.org: You start from PDB input file(s), where
>> atom and residue names are (more or less correctly) defined (by the
>> user). You execute Ante_R.E.D. to generate P2N file(s) from these
>> PDB input file(s). From the P2N file(s) mol2 files are generated by
>> R.E.D. Then, these mol2 files are loaded in LEaP (& associated with
>> a selected force field and other FF libraries; atom types are also
>> added in LEaP at this stage: see below) to generate the
>> prmtop/prmcrd files for a complex molecular system; these
>> prmtop/prmcrd files are directly used for MD simulations using
>> sander/pmemd (AMBER) or indirectly used for MD simulations using
>> CHARMM.
>>
>>> Are these parameters, AMBER parameters or CHARMM's?! Does it mean
>>> till producing Mol2/Mol3 files nothing different is going on?!
>>
>> mol2 vs mol3: see http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
>>
>> mol2 file: see http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
>>
>> I would like to underline that the 'savemol2' command has been
>> incorporated in LEaP by C. Cezard at q4md-forcefieldtools.org; we
>> also have developed the mol3 file format.
>>
>>> Then how these files turn into "rtf" format? Is it just rtf
>>> format with AMBER parameters or CHARMM parameters. As you know
>>> for sure these two force fields have totally different parameters.
>>
>> The mol2 files generated by R.E.D. does not contain any FF parameter!
>>
>> savemol2 unit mol2filename option
>> -> utility of the 'option' add or not add the FF atom types of a
>> given force field
>>
>> These FF atom types are added using a LEaP script...
>> See all the projects in R.E.DD.B. for instance W-46:
>> http://q4md-forcefieldtools.org/REDDB/projects/W-46/
>> & its LEaP script:
>> http://q4md-forcefieldtools.org/REDDB/projects/W-46/script1.ff
>> where the FF atom types ... for the Cornell et al. FF are defined.
>>
>> I am sure you can invent your own story for mol2 vs mol3 vs rtf
>> file formats and AMBER vs CHARMM ;-)
>>
>> The new version of R.E.D. (we are working on) will handled many new
>> features (& the P2N & mol2 files will not be used anymore).
>>
>>> This is exactly what I am trying to do:
>>
>> I understand ;-)
>>
>>> Find the AMBER parameters for an antibiotic which is inside a
>>> ribosome. I have AMBER parameters for ribosome in "CHARMM format"
>>> (because I run MD in NAMD and it needs CHARMM format). I need to
>>> have something similar for the antibiotic. Basically AMBER
>>> parameters, but once I got them I have to change the format to
>>> "CHARMM"'s.
>>
>> "find the AMBER parameters"? I would answer you have to validate
>> the AMBER parameters in the CHARMM context...
>>
>> regards, Francois
>>
>>
>>> On Sep 5, 2012, at 2:15 AM, FyD wrote:
>>>
>>>> Dear Rezvan,
>>>>
>>>>> I want to have the parameters for antibiotics bonded to
>>>>> ribosomes. I was wondering if I have to use ANTECHAMBER?
>>>>
>>>> You can use Antechamber and/or R.E.D. (or R.E.D. Server) at
>>>> http://q4md-forcefieldtools.org.
>>>>
>>>> I would like to suggest you to use R.E.D. (or R.E.D. Server). If
>>>> your antibiotics are connected through a bond to a larger system,
>>>> I suggest you twice to use R.E.D. ;-) as you will have to define
>>>> charge constraints during the charge fitting step.
>>>>
>>>>> I mean shall I produce the parameters myself?
>>>>
>>>> If they are not available: Yes
>>>>
>>>>> Have it been done before? Do parameters for antibiotics already
>>>>> exist in a par/topology file?
>>>>
>>>> In general you start from a PDB file and you generate a FF
>>>> library (off, mol2 or prep format) using R.E.D. or Antechamber
>>>> for your molecule; you load this new FF library in the LEaP
>>>> program (with the FF you wish to use) and create the
>>>> prmtop/prmcrd files for your entire molecular system for MD
>>>> simulation.
>>>>
>>>> Concerning using R.E.D. see:
>>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
>>>> or
>>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#1
>>>>
>>>>> By the way, I am not still sure. To use the ANTECHAMBER do I
>>>>> need to buy the AMBER program?!
>>>>
>>>> Antechamber and R.E.D. are provided at no cost; R.E.D. is free.
>>>> Antechamber is in the AmberTools (most of these tools are free).
>>>>
>>>> regards, Francois
>>
>>
>
>
>
>
> ------------------------------
>
> Message: 24
> Date: Fri, 14 Sep 2012 14:40:33 -0400
> From: Jonathan Gough <jonathan.d.gough.gmail.com>
> Subject: [AMBER] performance of pmed.cuda.MPI
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAFkCv1S-C=cfW6b_bsvX5h4XipCLE0gGS8A+nY4XbJ7279JJ3A.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear All,
>
> I'm curious if anyone is using a nvidia GTX 690 card. It has 2 cuda cores
> on it, and when using pmed.cuda.MPI I am not getting much of a speed bump
> when using both cores.
>
> Curious if others have experienced this or if there is something that I am
> missing, or maybe this is what to expect. Just asking...
>
> Jonathan
>
> for example - on the benchmarks - using the standard inputs and
> pmed.cuda.MPI:
>
> GB-myoglobin
> 1 core - ns/day = 144.09
> 2 core - ns/day = 156.14
>
> TRPCage
> 1 core - ns/day = 698.11
> 2 core - ns/day = 527.23
>
> Cellulose_prod_NPT
> 1 core - ns/day = 3.60
> 2 core - ns/day = 4.39
>
> JAC_production_NPT
> 1 core - ns/day = 57.33
> 2 core - ns/day = 67.92
>
> JAC_production_NVE
> 1 core - ns/day = 72.42
> 2 core - ns/day = 80.76
>
> FactorIX_production_NPT
> 1 core - ns/day = 15.57
> 2 core - ns/day = 18.50
>
>
> ------------------------------
>
> Message: 25
> Date: Fri, 14 Sep 2012 11:46:28 -0700
> From: Scott Le Grand <varelse2005.gmail.com>
> Subject: Re: [AMBER] performance of pmed.cuda.MPI
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAOU=08cjqPxOixuuN2r6asZKSLcawvjhj3USaPS_Bm0dk48UGw.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> MPI performance of GTX 690 is abysmal because the two GPUs share the same
> PCIEX adaptor.
>
> That will improve down the road somewhat.
>
> In the meantime, I think you'll be happy at the performance of two
> independent runs (one on each GPU): 98+% efficiency when I last checked...
>
>
> On Fri, Sep 14, 2012 at 11:40 AM, Jonathan Gough <jonathan.d.gough.gmail.com
>> wrote:
>
>> Dear All,
>>
>> I'm curious if anyone is using a nvidia GTX 690 card. It has 2 cuda cores
>> on it, and when using pmed.cuda.MPI I am not getting much of a speed bump
>> when using both cores.
>>
>> Curious if others have experienced this or if there is something that I am
>> missing, or maybe this is what to expect. Just asking...
>>
>> Jonathan
>>
>> for example - on the benchmarks - using the standard inputs and
>> pmed.cuda.MPI:
>>
>> GB-myoglobin
>> 1 core - ns/day = 144.09
>> 2 core - ns/day = 156.14
>>
>> TRPCage
>> 1 core - ns/day = 698.11
>> 2 core - ns/day = 527.23
>>
>> Cellulose_prod_NPT
>> 1 core - ns/day = 3.60
>> 2 core - ns/day = 4.39
>>
>> JAC_production_NPT
>> 1 core - ns/day = 57.33
>> 2 core - ns/day = 67.92
>>
>> JAC_production_NVE
>> 1 core - ns/day = 72.42
>> 2 core - ns/day = 80.76
>>
>> FactorIX_production_NPT
>> 1 core - ns/day = 15.57
>> 2 core - ns/day = 18.50
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> ------------------------------
>
> Message: 26
> Date: Fri, 14 Sep 2012 14:50:07 -0400
> From: Jonathan Gough <jonathan.d.gough.gmail.com>
> Subject: Re: [AMBER] performance of pmed.cuda.MPI
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAFkCv1RAG64pC=7_H+netD3auo6n24rtYgu1gTgMCrAsJcuP2A.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Thanks Scott. That makes a lot of sense.
>
> On Fri, Sep 14, 2012 at 2:46 PM, Scott Le Grand <varelse2005.gmail.com>wrote:
>
>> MPI performance of GTX 690 is abysmal because the two GPUs share the same
>> PCIEX adaptor.
>>
>> That will improve down the road somewhat.
>>
>> In the meantime, I think you'll be happy at the performance of two
>> independent runs (one on each GPU): 98+% efficiency when I last checked...
>>
>>
>> On Fri, Sep 14, 2012 at 11:40 AM, Jonathan Gough <
>> jonathan.d.gough.gmail.com
>> > wrote:
>>
>> > Dear All,
>> >
>> > I'm curious if anyone is using a nvidia GTX 690 card. It has 2 cuda
>> cores
>> > on it, and when using pmed.cuda.MPI I am not getting much of a speed bump
>> > when using both cores.
>> >
>> > Curious if others have experienced this or if there is something that I
>> am
>> > missing, or maybe this is what to expect. Just asking...
>> >
>> > Jonathan
>> >
>> > for example - on the benchmarks - using the standard inputs and
>> > pmed.cuda.MPI:
>> >
>> > GB-myoglobin
>> > 1 core - ns/day = 144.09
>> > 2 core - ns/day = 156.14
>> >
>> > TRPCage
>> > 1 core - ns/day = 698.11
>> > 2 core - ns/day = 527.23
>> >
>> > Cellulose_prod_NPT
>> > 1 core - ns/day = 3.60
>> > 2 core - ns/day = 4.39
>> >
>> > JAC_production_NPT
>> > 1 core - ns/day = 57.33
>> > 2 core - ns/day = 67.92
>> >
>> > JAC_production_NVE
>> > 1 core - ns/day = 72.42
>> > 2 core - ns/day = 80.76
>> >
>> > FactorIX_production_NPT
>> > 1 core - ns/day = 15.57
>> > 2 core - ns/day = 18.50
>> > _______________________________________________
>> > 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 274, Issue 1
> *************************************
>
>
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Received on Sat Sep 15 2012 - 02:30:03 PDT
