Thanks!
At 2016-11-21 04:00:02, amber-request.ambermd.org wrote:
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>AMBER Mailing List Digest
>
>Today's Topics:
>
> 1. TUTORIAL B5: Simulating the Green Fluorescent Protein
> -PREPGEN Error (Taylor, Miles)
> 2. Re: Query regarding the MCPB.py workflow (Abhi Acharya)
> 3. Re: MM-GBSA calculation in temperature other than 298.15 K
> (Atila Petrosian)
> 4. Re: MM-GBSA calculation in temperature other than 298.15 K
> (Daniel Roe)
> 5. Re: TUTORIAL B5: Simulating the Green Fluorescent Protein
> -PREPGEN Error (Brent Krueger)
> 6. How to change the dielectric constant in the electrostatic
> energy term? (???)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Sat, 19 Nov 2016 16:50:20 -0800
>From: "Taylor, Miles" <taylormi.oregonstate.edu>
>Subject: [AMBER] TUTORIAL B5: Simulating the Green Fluorescent Protein
> -PREPGEN Error
>To: amber.ambermd.org
>Message-ID:
> <CAK1=UJPg8qrBD-FpOP3hQuW1Q_UVxYneR-=b=bi6CQk=Q0wStw.mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Dear Amber,
>
>I am writing to you because I am following this tutorial:
>http://ambermd.org/tutorials/basic/tutorial5/
>
>This tutorial uses the CRO chromophore (Ser-Tyr-Gly):
>https://www3.rcsb.org/ligand/CRO
>
>While I am instead using the NRQ chromophore (Met-Tyr-Gly):
>https://www3.rcsb.org/ligand/NRQ
>
>I am on the step that uses Prepgen to eliminate certain residues and it
>continues to fail. Here is the command I am running:
>
>prepgen -i NRQ.ac -o NRQ.prepin -m NRQ.mc -rn NRQ
>
>Also, here is the NRQ.mc file that I created:
>
>HEAD_NAME N1
>TAIL_NAME C3
>MAIN_CHAIN CA1
>MAIN_CHAIN C1
>MAIN_CHAIN N3
>MAIN_CHAIN CA3
>OMIT_NAME H2
>OMIT_NAME OXT
>OMIT_NAME HXT
>PRE_HEAD_TYPE C
>POST_TAIL_TYPE N
>CHARGE 0.0
>
>It seems that every time I run the file I get this output or a similar
>error output:
>
>PRE_HEAD_TYPE is C
>POST_TAIL_TYPE is N
>Net charge of truncated molecule is 0.00
>HEAD_ATOM 1 N1
>TAIL_ATOM 22 C3
>MAIN_CHAIN 1 1 N1
>MAIN_CHAIN 2 6 CA1
>MAIN_CHAIN 3 7 C1
>MAIN_CHAIN 4 20 N3
>MAIN_CHAIN 5 21 CA3
>MAIN_CHAIN 6 22 C3
>OMIT_ATOM 1 25 H2
>OMIT_ATOM 2 24 OXT
>OMIT_ATOM 3 41 HXT
>Number of mainchain atoms (including head and tail atom): 6
>Segmentation fault (core dumped)
>
>Prepgen seems to be adding the "MAIN_CHAIN 1 1 N1" and "MAIN_CHAIN
> 6 22 C3" lines with every attempt. I tried removing all Main_Chains
>and it still adds them, I tried adding them beforehand and it duplicated
>them.
>
>I am having a little difficulty. Please help.
>
>Thank you.
>
>Sincerely,
>Miles Taylor
>Graduate Student
>Physical Chemistry
>
>
>------------------------------
>
>Message: 2
>Date: Sun, 20 Nov 2016 12:04:34 +0530
>From: Abhi Acharya <abhi117acharya.gmail.com>
>Subject: Re: [AMBER] Query regarding the MCPB.py workflow
>To: amber.ambermd.org
>Message-ID:
> <CAB1aw3zdV3L=RYTKf8sf4iVRjXqrL=EAWdpwnawS=Brv6q_Xqw.mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Hello Dr. Pengfei.
>
>I made the suggested changes to the code. However, this time I am getting a
>different error saying that the charges and atoms do not match.
>
>Here is the output:
>
>The input file you are using is : 3UJO.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>The following is the input variable you have:
>The variable ion_ids is : [3825, 3826]
>The variable ion_info is : []
>The variable ion_mol2files is : ['CA.mol2', 'CU.mol2']
>The variable original_pdb is : 3UJO_fixed_H.pdb
>The variable add_bonded_pairs is : []
>The variable additional_resids is : []
>The variable anglefc_avg is : 0
>The variable bondfc_avg is : 0
>The variable cut_off is : 2.8
>The variable chgfix_resids is : []
>The variable force_field is : ff14SB
>The variable frcmodfs is : []
>The variable gaff is : 1
>The variable group_name is : 3UJO
>The variable ion_paraset is : CM (Only for nonbonded model)
>The variable large_opt is : 1
>The variable lgmodel_chg is : -99
> -99 means program will assign a charge automatically.
>The variable naa_mol2files is : ['WAT.mol2']
>The variable scale_factor is : 1.0
> ATTENTION: This is the scale factor of frequency. The
> force constants will be scaled by multiplying the square
> of scale_factor.
>The variable smmodel_chg is : -99
> -99 means program will assign a charge automatically.
>The variable software_version is : gms
>The variable sqm_opt is : 0
>The variable water_model is : TIP3P
>******************************************************************
>* *
>*======================RESP Charge fitting=======================*
>* *
>******************************************************************
>***Generating the 1st stage resp charge fitting input file...
>***Generating the 2nd stage resp charge fitting input file...
>***Doing the RESP charge fiting...
>CAUTION: THE VDW RADIUS OF ATOMIC NUMBER 20IS UNKNOWN AND HAS
>BEEN SET TO1.80 ANGSTROMS IN THE GAMESS CALCULATION.
>CAUTION: THE VDW RADIUS OF ATOMIC NUMBER 29IS UNKNOWN AND HAS
>BEEN SET TO1.80 ANGSTROMS IN THE GAMESS CALCULATION.
>=========================Checking models==========================
>***Check the large model...
>Good. The charges and atom numbers are match for the large model.
>Good. There are 186 atoms in the large model.
>***Check the standard model...
>Traceback (most recent call last):
> File "/home/bp-lab/install-fold/amber16/bin/MCPB.py", line 600, in
><module>
> premol2fs, mcresname, 1, chgfix_resids, g0x, lgchg)
> File
>"/home/bp-lab/install-fold/amber16/lib/python2.7/site-packages/mcpb/resp_fitting.py",
>line 517, in resp_fitting
> raise pymsmtError('Error: the charges and atom numbers are mismatch '
>pymsmtexp.pymsmtError: Error: the charges and atom numbers are mismatch for
>the standard model!
>
>Kindly help.
>
>Best Regards,
>Abhishek
>
>On Wed, Nov 16, 2016 at 4:15 PM, Abhi Acharya <abhi117acharya.gmail.com>
>wrote:
>
>> Hello Amber users,
>>
>> Perhaps my question was not clear previously.
>>
>> I have been trying to calculate charges for active site metal ions and the
>> coordinating residues using the seminario method. i follow the tutorial by
>> Pengfei et al.
>>
>> These are the steps I followed:
>>
>> 1. created the pdb for the protein model with Hydrogens added. Also
>> created the mol2 files for active site water molecules (single file with 4
>> molecules) and ions (one each for Cu and Ca ion).
>> 2. Next I proceeded to generate the small and large active site models
>> using GAMESS.
>> 3. Performed geometry optimization and fc calculation for small model.
>> Optimized the large model and performed charge calculations using GAMESS.
>> 4. Generated the frcmod file for the active site using the command:
>> MCPB.py -i input.in -s 2
>>
>> So far so good. My problem is the following:
>> A. How to proceed after creating the initial frcmod file i.e after the
>> second step MCPB.py -i input -s 2. Everything works smoothly till this
>> step. However, in the next step:
>>
>> MCPB.py -i input -s 3
>>
>> I get the following error:
>> The following is the input variable you have:
>> The variable ion_ids is : [3825, 3826]
>> The variable ion_info is : []
>> The variable ion_mol2files is : ['CA.mol2', 'CU.mol2']
>> The variable original_pdb is : 3UJO_fixed_H.pdb
>> The variable add_bonded_pairs is : []
>> The variable additional_resids is : []
>> The variable anglefc_avg is : 0
>> The variable bondfc_avg is : 0
>> The variable cut_off is : 2.8
>> The variable chgfix_resids is : []
>> The variable force_field is : ff14SB
>> The variable frcmodfs is : []
>> The variable gaff is : 1
>> The variable group_name is : 3UJO
>> The variable ion_paraset is : CM (Only for nonbonded model)
>> The variable large_opt is : 1
>> The variable lgmodel_chg is : -99
>> -99 means program will assign a charge automatically.
>> The variable naa_mol2files is : ['WAT.mol2']
>> The variable scale_factor is : 1.0
>> ATTENTION: This is the scale factor of frequency. The
>> force constants will be scaled by multiplying the square
>> of scale_factor.
>> The variable smmodel_chg is : -99
>> -99 means program will assign a charge automatically.
>> The variable software_version is : gms
>> The variable sqm_opt is : 0
>> The variable water_model is : TIP3P
>> ******************************************************************
>> * *
>> *======================RESP Charge fitting=======================*
>> * *
>> ******************************************************************
>> ***Generating the 1st stage resp charge fitting input file...
>> ***Generating the 2nd stage resp charge fitting input file...
>> ***Doing the RESP charge fiting...
>> Traceback (most recent call last):
>> File "/home/bp-lab/install-fold/amber16/bin/MCPB.py", line 600, in
>> <module>
>> premol2fs, mcresname, 1, chgfix_resids, g0x, lgchg)
>> File "/home/bp-lab/install-fold/amber16/lib/python2.7/site-
>> packages/mcpb/resp_fitting.py", line 443, in resp_fitting
>> get_esp_from_gms(mklogf, espf)
>> File "/home/bp-lab/install-fold/amber16/lib/python2.7/site-packages/msmtmol/gmsio.py",
>> line 222, in get_esp_from_gms
>> for i in range(bln, eln+1):
>> UnboundLocalError: local variable 'eln' referenced before assignment
>>
>>
>> B. I did not find any mol2 files generated for the active site
>> coordinating residues. Perhaps, these files will be generated if the above
>> errors are rectified.
>> Am I correct?
>>
>>
>> Kindly help.
>>
>>
>> Thanks and Regards,
>> Abhishek Acharya
>>
>> On Sat, Nov 12, 2016 at 2:39 PM, Abhi Acharya <abhi117acharya.gmail.com>
>> wrote:
>>
>>> Hi amber users,
>>>
>>> I am trying to use the MCPB.py workflow to derive parameters for an
>>> active site containing Cu2+ and Ca2+ ions. The Cu2+ ion is coordinated by
>>> two water molecules, and active site residues Asp, His etc.
>>> My question is that in the input file for MCPB.py do we need to specify
>>> separate mol2 files for the two water molecules and the coordinating
>>> residues? In the MCPB.py tutorial at this link:
>>> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm the input
>>> file does not specify any of the coordinating His residues. But still in
>>> the 3rd step i.e. MCPB.py -i 1OKL.in -s 3, the tutorial says that mol2
>>> files for HD1, HD2 and HE1 will be created. I am a bit confused.
>>>
>>> I request you to kindly clarify this.
>>>
>>> Thanks and Regards,
>>> Abhishek Acharya
>>> CFTRI, Mysore.
>>>
>>
>>
>
>
>------------------------------
>
>Message: 3
>Date: Sun, 20 Nov 2016 12:22:52 +0330
>From: Atila Petrosian <atila.petrosian.gmail.com>
>Subject: Re: [AMBER] MM-GBSA calculation in temperature other than
> 298.15 K
>To: AMBER Mailing List <amber.ambermd.org>
>Message-ID:
> <CAON_0oV4Uz9vHw9bM+VELY6RyokzFEDUdpXp=F9mDtptc0NfeQ.mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Dear Dan,
>
>Thanks for your answer.
>
>> What version of AmberTools are you using?
>
>I'm using AmberTools 14.
>
>> I'm pretty certain the 298 K temperature restriction was removed sone
>time ago.
>
>Are you sure??? There is the following sentence in MM-GBSA output file.
>|All entropy results have units kcal/mol (Temperature is 298.15 K).
>
>
>Dear Jason,
>
>Thanks for your answer.
>
>>> 1. The trajectory must be run at the desired temperature to ensure the
>proper
>>> Boltzmann distribution of snapshots at that temperature. This is all
>that's
>>> necessary to get the "correct" PB or GB energies at the desired
>temperature.
>
>I ran MD simulation at the desired temperature (310 K).
>
>>> 2. For quasi-harmonic analysis, the temperature needs to be provided to
>cpptraj.
>>> However, MMPBSA.py does not expose this variable, since ptraj did not
>support specifying
>>> the temperature at the time that MMPBSA.py was written.So you need to
>change the MMPBSA.py source code to modify the input file given to cpptraj
>(create_input.py).
>
>I'm a beginner in modifying source codes. Please help me to do that step by
>step.
>Is not a tutorial about doing MM-GBSA at different temperatures?
>
>Thanks,
>Atila
>
>On Thu, Nov 17, 2016 at 9:25 PM, Jason Swails <jason.swails.gmail.com>
>wrote:
>
>> As things stand now, temperature comes into play in 3 places:
>>
>> 1. The trajectory must be run at the desired temperature to ensure the
>> proper Boltzmann distribution of snapshots at that temperature. This is all
>> that's necessary to get the "correct" PB or GB energies at the desired
>> temperature.
>>
>> 2. For quasi-harmonic analysis, the the temperature needs to be provided to
>> cpptraj. However, MMPBSA.py does not expose this variable, since ptraj did
>> not support specifying the temperature at the time that MMPBSA.py was
>> written. So you need to change the MMPBSA.py source code to modify the
>> input file given to cpptraj (create_input.py)
>>
>> 3. For normal mode calculation, nab itself is hard-coded to use 298.15 as
>> temperature in several places (look in nmode.c in
>> $AMBERHOME/AmberTools/src/sff). You will need to adjust the code with the
>> new temperature, then recompile AmberTools.
>>
>> For both 2 and 3, you will need to modify the MMPBSA.py source code to
>> specify a different temperature (this only affects what the entropy results
>> get multiplied by). Look for line 765 of main.py.
>>
>> The take-home message is that changing temperatures for entropy calculation
>> in MMPBSA.py is not easy, and you should carefully check that any changes
>> you make have the expected effect. The first piece of advice to performing
>> MM/PBSA analyses is to make sure you can do it "by hand" first, before
>> using either of the scripts. That is particularly good advice here.
>>
>> HTH,
>> Jason
>>
>> On Thu, Nov 17, 2016 at 8:22 AM, Atila Petrosian <
>> atila.petrosian.gmail.com>
>> wrote:
>>
>> > Excuse me. Considered temperature is 330 K in my project.
>> >
>> > On Thu, Nov 17, 2016 at 4:42 PM, Atila Petrosian <
>> > atila.petrosian.gmail.com>
>> > wrote:
>> >
>> > > Dear Carlos,
>> > >
>> > > Thanks for your answer.
>> > >
>> > > I did MD simulation of my system (protein-ligand complex) in 330 K.
>> Thus,
>> > > I have the trajectory data at the temperature (300 K) I want. Now, I
>> want
>> > > to do Binding free energy and have entropy in 300 K. How to do that?
>> > >
>> > > Any help will highly appreciated to help me to consider both of issues.
>> > >
>> > > Best,
>> > > Atila
>> > >
>> > > On Thu, Nov 17, 2016 at 4:05 PM, Carlos Simmerling <
>> > > carlos.simmerling.gmail.com> wrote:
>> > >
>> > >> the answers seem to address different things - Adrian mentions needing
>> > to
>> > >> have trajectory data at the temperature you want. Jason is talking
>> about
>> > >> the actual MM-PBSA program and how it needs to be changed if you want
>> > >> entropies at a different T.
>> > >> I think both of these are things you should consider.
>> > >>
>> > >>
>> > >> On Thu, Nov 17, 2016 at 1:46 AM, Atila Petrosian <
>> > >> atila.petrosian.gmail.com>
>> > >> wrote:
>> > >>
>> > >> > Dear Carlos,
>> > >> >
>> > >> > I checked archive. Jason Swail answer is as follows:
>> > >> >
>> > >> > Not easily. You need to modify source codes to change the
>> temperature.
>> > >> The
>> > >> > vibrational and rotational entropies are computed via statistical
>> > >> > mechanical formulae that assume a particular temperature (and for
>> > >> > quasi-harmonic entropies, you really need to use the temperature
>> that
>> > >> the
>> > >> > simulation was run at). And last time I checked, this temperature
>> was
>> > >> > hard-coded directly into the program, so you would need to change
>> the
>> > >> > original source code and recompile, as well as
>> > >> > modify the temperature variable in MMPBSA.py, in order to try a
>> > >> different
>> > >> > temperature.
>> > >> >
>> > >> > But I found same question from another person (Shahab Shariati):
>> > MM-PBSA
>> > >> > calculation in different temprature:
>> > >> >
>> > >> > Adrian Roitberg answer is as follows:
>> > >> >
>> > >> > Technically yes, you have to RERUN the MD at the new temperature and
>> > >> rerun
>> > >> > mmpbsa. You should not reuse the MD at 298 and simply change the
>> > >> > temperature in mmbpsa. However, it is extremely unlikely that you
>> will
>> > >> see
>> > >> > statistically meaningful differences between 298 and 310 with
>> mmbpsa.
>> > >> >
>> > >> > I encontered with 2 different answers. Finally, is it possible to do
>> > >> > MM-GBSA in temperature other than 298.15 K?
>> > >> >
>> > >> > Best,
>> > >> > Atila
>> > >> >
>> > >> > On Wed, Nov 16, 2016 at 2:42 PM, Carlos Simmerling <
>> > >> > carlos.simmerling.gmail.com> wrote:
>> > >> >
>> > >> > > Always check the archives before sending email. This has been
>> > >> discussed
>> > >> > > extensively before, and you can read the answers by typing
>> "Mm-gbsa
>> > >> > > temperature" in the search box on the amber web site.
>> > >> > >
>> > >> > > On Nov 16, 2016 12:42 AM, "Atila Petrosian" <
>> > >> atila.petrosian.gmail.com>
>> > >> > > wrote:
>> > >> > >
>> > >> > > > Dear Amber users.
>> > >> > > >
>> > >> > > > I did MD simulation of my system (protein-ligand complex) in 330
>> > K.
>> > >> > > >
>> > >> > > > I used obtained trajectory for MM-GBSA calculation. But in
>> output
>> > >> file
>> > >> > > > (*.dat), there is
>> > >> > > >
>> > >> > > > |All units are reported in kcal/mole.
>> > >> > > > |All entropy results have units kcal/mol (Temperature is 298.15
>> > K).
>> > >> > > >
>> > >> > > > I want to have Binding free energy in 330 K and not 298.15 K.
>> > >> > > >
>> > >> > > > How to resolve that.
>> > >> > > >
>> > >> > > > Best,
>> > >> > > > Atila
>> > >> > > > _______________________________________________
>> > >> > > > 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
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>------------------------------
>
>Message: 4
>Date: Sun, 20 Nov 2016 07:05:06 -0500
>From: Daniel Roe <daniel.r.roe.gmail.com>
>Subject: Re: [AMBER] MM-GBSA calculation in temperature other than
> 298.15 K
>To: AMBER Mailing List <amber.ambermd.org>
>Message-ID:
> <CAAC0qObjPZ0uCSNbMX65MKOzM8L3dzzAhaTLWWCOWKowxQNYcg.mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>On Sun, Nov 20, 2016 at 3:52 AM, Atila Petrosian
><atila.petrosian.gmail.com> wrote:
>>> I'm pretty certain the 298 K temperature restriction was removed sone
>> time ago.
>>
>> Are you sure??? There is the following sentence in MM-GBSA output file.
>> |All entropy results have units kcal/mol (Temperature is 298.15 K).
>
>To clarify; the temperature restriction was removed from the code in
>cpptraj that MMPBSA.py uses on the back-end for the quasi-harmonic
>calculation. In order to use it you will need to modify MMPBSA.py as
>Jason suggested.
>
>-Dan
>
>>
>>
>> Dear Jason,
>>
>> Thanks for your answer.
>>
>>>> 1. The trajectory must be run at the desired temperature to ensure the
>> proper
>>>> Boltzmann distribution of snapshots at that temperature. This is all
>> that's
>>>> necessary to get the "correct" PB or GB energies at the desired
>> temperature.
>>
>> I ran MD simulation at the desired temperature (310 K).
>>
>>>> 2. For quasi-harmonic analysis, the temperature needs to be provided to
>> cpptraj.
>>>> However, MMPBSA.py does not expose this variable, since ptraj did not
>> support specifying
>>>> the temperature at the time that MMPBSA.py was written.So you need to
>> change the MMPBSA.py source code to modify the input file given to cpptraj
>> (create_input.py).
>>
>> I'm a beginner in modifying source codes. Please help me to do that step by
>> step.
>> Is not a tutorial about doing MM-GBSA at different temperatures?
>>
>> Thanks,
>> Atila
>>
>> On Thu, Nov 17, 2016 at 9:25 PM, Jason Swails <jason.swails.gmail.com>
>> wrote:
>>
>>> As things stand now, temperature comes into play in 3 places:
>>>
>>> 1. The trajectory must be run at the desired temperature to ensure the
>>> proper Boltzmann distribution of snapshots at that temperature. This is all
>>> that's necessary to get the "correct" PB or GB energies at the desired
>>> temperature.
>>>
>>> 2. For quasi-harmonic analysis, the the temperature needs to be provided to
>>> cpptraj. However, MMPBSA.py does not expose this variable, since ptraj did
>>> not support specifying the temperature at the time that MMPBSA.py was
>>> written. So you need to change the MMPBSA.py source code to modify the
>>> input file given to cpptraj (create_input.py)
>>>
>>> 3. For normal mode calculation, nab itself is hard-coded to use 298.15 as
>>> temperature in several places (look in nmode.c in
>>> $AMBERHOME/AmberTools/src/sff). You will need to adjust the code with the
>>> new temperature, then recompile AmberTools.
>>>
>>> For both 2 and 3, you will need to modify the MMPBSA.py source code to
>>> specify a different temperature (this only affects what the entropy results
>>> get multiplied by). Look for line 765 of main.py.
>>>
>>> The take-home message is that changing temperatures for entropy calculation
>>> in MMPBSA.py is not easy, and you should carefully check that any changes
>>> you make have the expected effect. The first piece of advice to performing
>>> MM/PBSA analyses is to make sure you can do it "by hand" first, before
>>> using either of the scripts. That is particularly good advice here.
>>>
>>> HTH,
>>> Jason
>>>
>>> On Thu, Nov 17, 2016 at 8:22 AM, Atila Petrosian <
>>> atila.petrosian.gmail.com>
>>> wrote:
>>>
>>> > Excuse me. Considered temperature is 330 K in my project.
>>> >
>>> > On Thu, Nov 17, 2016 at 4:42 PM, Atila Petrosian <
>>> > atila.petrosian.gmail.com>
>>> > wrote:
>>> >
>>> > > Dear Carlos,
>>> > >
>>> > > Thanks for your answer.
>>> > >
>>> > > I did MD simulation of my system (protein-ligand complex) in 330 K.
>>> Thus,
>>> > > I have the trajectory data at the temperature (300 K) I want. Now, I
>>> want
>>> > > to do Binding free energy and have entropy in 300 K. How to do that?
>>> > >
>>> > > Any help will highly appreciated to help me to consider both of issues.
>>> > >
>>> > > Best,
>>> > > Atila
>>> > >
>>> > > On Thu, Nov 17, 2016 at 4:05 PM, Carlos Simmerling <
>>> > > carlos.simmerling.gmail.com> wrote:
>>> > >
>>> > >> the answers seem to address different things - Adrian mentions needing
>>> > to
>>> > >> have trajectory data at the temperature you want. Jason is talking
>>> about
>>> > >> the actual MM-PBSA program and how it needs to be changed if you want
>>> > >> entropies at a different T.
>>> > >> I think both of these are things you should consider.
>>> > >>
>>> > >>
>>> > >> On Thu, Nov 17, 2016 at 1:46 AM, Atila Petrosian <
>>> > >> atila.petrosian.gmail.com>
>>> > >> wrote:
>>> > >>
>>> > >> > Dear Carlos,
>>> > >> >
>>> > >> > I checked archive. Jason Swail answer is as follows:
>>> > >> >
>>> > >> > Not easily. You need to modify source codes to change the
>>> temperature.
>>> > >> The
>>> > >> > vibrational and rotational entropies are computed via statistical
>>> > >> > mechanical formulae that assume a particular temperature (and for
>>> > >> > quasi-harmonic entropies, you really need to use the temperature
>>> that
>>> > >> the
>>> > >> > simulation was run at). And last time I checked, this temperature
>>> was
>>> > >> > hard-coded directly into the program, so you would need to change
>>> the
>>> > >> > original source code and recompile, as well as
>>> > >> > modify the temperature variable in MMPBSA.py, in order to try a
>>> > >> different
>>> > >> > temperature.
>>> > >> >
>>> > >> > But I found same question from another person (Shahab Shariati):
>>> > MM-PBSA
>>> > >> > calculation in different temprature:
>>> > >> >
>>> > >> > Adrian Roitberg answer is as follows:
>>> > >> >
>>> > >> > Technically yes, you have to RERUN the MD at the new temperature and
>>> > >> rerun
>>> > >> > mmpbsa. You should not reuse the MD at 298 and simply change the
>>> > >> > temperature in mmbpsa. However, it is extremely unlikely that you
>>> will
>>> > >> see
>>> > >> > statistically meaningful differences between 298 and 310 with
>>> mmbpsa.
>>> > >> >
>>> > >> > I encontered with 2 different answers. Finally, is it possible to do
>>> > >> > MM-GBSA in temperature other than 298.15 K?
>>> > >> >
>>> > >> > Best,
>>> > >> > Atila
>>> > >> >
>>> > >> > On Wed, Nov 16, 2016 at 2:42 PM, Carlos Simmerling <
>>> > >> > carlos.simmerling.gmail.com> wrote:
>>> > >> >
>>> > >> > > Always check the archives before sending email. This has been
>>> > >> discussed
>>> > >> > > extensively before, and you can read the answers by typing
>>> "Mm-gbsa
>>> > >> > > temperature" in the search box on the amber web site.
>>> > >> > >
>>> > >> > > On Nov 16, 2016 12:42 AM, "Atila Petrosian" <
>>> > >> atila.petrosian.gmail.com>
>>> > >> > > wrote:
>>> > >> > >
>>> > >> > > > Dear Amber users.
>>> > >> > > >
>>> > >> > > > I did MD simulation of my system (protein-ligand complex) in 330
>>> > K.
>>> > >> > > >
>>> > >> > > > I used obtained trajectory for MM-GBSA calculation. But in
>>> output
>>> > >> file
>>> > >> > > > (*.dat), there is
>>> > >> > > >
>>> > >> > > > |All units are reported in kcal/mole.
>>> > >> > > > |All entropy results have units kcal/mol (Temperature is 298.15
>>> > K).
>>> > >> > > >
>>> > >> > > > I want to have Binding free energy in 330 K and not 298.15 K.
>>> > >> > > >
>>> > >> > > > How to resolve that.
>>> > >> > > >
>>> > >> > > > Best,
>>> > >> > > > Atila
>>> > >> > > > _______________________________________________
>>> > >> > > > 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
>>> >
>>>
>>>
>>>
>>> --
>>> Jason M. Swails
>>> _______________________________________________
>>> 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
>
>
>
>--
>-------------------------
>Daniel R. Roe
>Laboratory of Computational Biology
>National Institutes of Health, NHLBI
>5635 Fishers Ln, Rm T900
>Rockville MD, 20852
>https://www.lobos.nih.gov/lcb
>
>
>
>------------------------------
>
>Message: 5
>Date: Sun, 20 Nov 2016 09:31:59 -0500
>From: Brent Krueger <kruegerb.hope.edu>
>Subject: Re: [AMBER] TUTORIAL B5: Simulating the Green Fluorescent
> Protein -PREPGEN Error
>To: AMBER Mailing List <amber.ambermd.org>
>Message-ID:
> <CAPjhn9cAp2uAPMeYPwB9DifE9dZfYbM_gir7X61Mbm2Cvd-F0w.mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Miles,
>
>I'm afraid I can't help you with these prepgen issues, but I would like to
>point out that AMBER now has built-in parameters for a number of
>fluorescent protein chromophores. These include EGFP with the CRO
>chromophore (and several other fluorescent proteins) that have Tyr and Gly
>as the 2nd and 3rd residues and also EBFP with the CR2 chromophore, which
>has Ser as the 1st residue. In AmberTools16 you can find the atoms types
>for all of these in the xFPchromophores.lib file and modified force field
>parameters in frcmod.xFPchromophores file. There is also a leaprc file
>that loads these files and sets up some atom types.
>
>The parameters for these xFPs were developed to be modular, so you may be
>able to use these atoms types and the frcmod file directly in your
>situation. The parameters are meant to work with ff14SB, but they utilize
>some atom types from GAFF, which is why the leaprc file needs to do a
>little bit more than just load the lib and frcmod files. You will need to
>calculate charges for the atoms as these are unique for every situation.
>
>Again, sorry I can't help with prepgen, but if you want any assistance with
>atom types, etc. feel free to send me a note directly (off the amber
>mailing list).
>
>
>Cheers,
>Brent
>
>
>
>On Sat, Nov 19, 2016 at 7:50 PM, Taylor, Miles <taylormi.oregonstate.edu>
>wrote:
>
>> Dear Amber,
>>
>> I am writing to you because I am following this tutorial:
>> http://ambermd.org/tutorials/basic/tutorial5/
>>
>> This tutorial uses the CRO chromophore (Ser-Tyr-Gly):
>> https://www3.rcsb.org/ligand/CRO
>>
>> While I am instead using the NRQ chromophore (Met-Tyr-Gly):
>> https://www3.rcsb.org/ligand/NRQ
>>
>> I am on the step that uses Prepgen to eliminate certain residues and it
>> continues to fail. Here is the command I am running:
>>
>> prepgen -i NRQ.ac -o NRQ.prepin -m NRQ.mc -rn NRQ
>>
>> Also, here is the NRQ.mc file that I created:
>>
>> HEAD_NAME N1
>> TAIL_NAME C3
>> MAIN_CHAIN CA1
>> MAIN_CHAIN C1
>> MAIN_CHAIN N3
>> MAIN_CHAIN CA3
>> OMIT_NAME H2
>> OMIT_NAME OXT
>> OMIT_NAME HXT
>> PRE_HEAD_TYPE C
>> POST_TAIL_TYPE N
>> CHARGE 0.0
>>
>> It seems that every time I run the file I get this output or a similar
>> error output:
>>
>> PRE_HEAD_TYPE is C
>> POST_TAIL_TYPE is N
>> Net charge of truncated molecule is 0.00
>> HEAD_ATOM 1 N1
>> TAIL_ATOM 22 C3
>> MAIN_CHAIN 1 1 N1
>> MAIN_CHAIN 2 6 CA1
>> MAIN_CHAIN 3 7 C1
>> MAIN_CHAIN 4 20 N3
>> MAIN_CHAIN 5 21 CA3
>> MAIN_CHAIN 6 22 C3
>> OMIT_ATOM 1 25 H2
>> OMIT_ATOM 2 24 OXT
>> OMIT_ATOM 3 41 HXT
>> Number of mainchain atoms (including head and tail atom): 6
>> Segmentation fault (core dumped)
>>
>> Prepgen seems to be adding the "MAIN_CHAIN 1 1 N1" and "MAIN_CHAIN
>> 6 22 C3" lines with every attempt. I tried removing all Main_Chains
>> and it still adds them, I tried adding them beforehand and it duplicated
>> them.
>>
>> I am having a little difficulty. Please help.
>>
>> Thank you.
>>
>> Sincerely,
>> Miles Taylor
>> Graduate Student
>> Physical Chemistry
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
>--
>_______________________________________________
>Brent P. Krueger.....................phone: 616 395 7629
>Professor.................................fax: 616 395 7118
>Hope College..........................Schaap Hall 2120
>Department of Chemistry
>Holland, MI 49423
>
>
>------------------------------
>
>Message: 6
>Date: Mon, 21 Nov 2016 00:02:05 +0800 (CST)
>From: ??? <fgq0708.163.com>
>Subject: [AMBER] How to change the dielectric constant in the
> electrostatic energy term?
>To: amber.ambermd.org
>Message-ID: <4bf5f399.5d10.15882791f21.Coremail.fgq0708.163.com>
>Content-Type: text/plain; charset=GBK
>
>Dear everyone,
>I want to chage the dielectric constant to 5 in the electrostatic energy term?
>and can I change the value of charges in top file?
>And then is each atom?s charge divided by sqrt(5)?
> or which subprogram can be modified in amber to chage the dielectric constant?
>Thank you!
>
>By Feng G. Q. from SDNU, Jinan, China.
>
>
>
>
>
>
>
>------------------------------
>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
>
>
>End of AMBER Digest, Vol 1763, Issue 1
>**************************************
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Received on Tue Nov 22 2016 - 01:00:03 PST
