Hi,
The cpptraj version is 18.01.
Jason M. Imamoto
Doctoral Candidate
Department of Chemistry and Biochemistry
GH 302
University of the Sciences in Philadelphia
600 S 43rd St. Philadelphia, PA 19104
Email: jimamoto.mail.usciences.edu
> On Mar 18, 2019, at 3:00 PM, amber-request.ambermd.org wrote:
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> Today's Topics:
>
> 1. A confused question about calculate the binding free energy
> from MMPBSA.py (bjyx20090941)
> 2. Re: Amber18 STSM (Feng Pan)
> 3. Re: velocities from and velocityautocorr (Ruth Helena Tichauer)
> 4. Re: gaff2 parameters of c3-c3-os-c3 (Tr?g)
> 5. Installation Problem (david stephen)
> 6. Re: Installation Problem (Bill Ross)
> 7. Re: Installation Problem (Gerardo Zerbetto De Palma)
> 8. Re: Installation Problem (Bill Ross)
> 9. pdb file with 4 atoms coordinates of water molecules with
> TIP4PFB model (bjyx20090941)
> 10. Re: pdb file with 4 atoms coordinates of water molecules with
> TIP4PFB model (Daniel Roe)
> 11. Assigning protonation states manually to the amino vs CpH MD
> simulation (Bharat Manna)
> 12. Re: Assigning protonation states manually to the amino vs CpH
> MD simulation (Carlos Simmerling)
> 13. Nastruct vs 3DNA (Jason Imamoto)
> 14. Re: Nastruct vs 3DNA (Daniel Roe)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 18 Mar 2019 09:13:28 +0800 (CST)
> From: bjyx20090941 <bjyx20090941.163.com>
> Subject: [AMBER] A confused question about calculate the binding free
> energy from MMPBSA.py
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID: <5cae4208.3288.1698e5c4f81.Coremail.bjyx20090941.163.com>
> Content-Type: text/plain; charset=GBK
>
> Dear amber:
> I have a confused question about calculate the binding free energy from MMPBSA.py.
>
> Recently, I am learning how to calculate the binding free energy of receptor-ligand complex in solvated environment with MMPBSA module. And now I am repeating the example of ras-raf complex in amber tutorial. But I am confused by the result as follows due to the different versions of amber, such in tutorial the result is came from amber10,and my result is come from amber16.
>
> I found that some parameters have changed as default values, example parameters of inp and radiopt. I have compared the results in listed:
>
> Table 1.The average binding free energy without entropy effect of 50 frames from different amber versions (kcal/mol?
>
> |
>
>
>
> |
>
> Amber10(yours)
>
> |
>
> Amber16(me)
>
> |
> |
>
> Different parameter
>
> |
>
> ipb=1,
>
> inp=1, radiopt=0
>
> |
>
> ipb=2,
>
> inp=2, radiopt=1
>
> |
> |
>
> ?Emm
>
> |
>
> -1025.4769
>
> |
>
> -1060.0425
>
> |
> |
>
> ?EPB
>
> |
>
> 946.4251
>
> |
>
> 978.3053
>
> |
> |
>
> ?ENpolar/Cavity
>
> |
>
> -7.3062
>
> |
>
> -51.5872
>
> |
> |
>
> ?Edisper
>
> |
>
> --
>
> |
>
> 102.4891
>
> |
> |
>
> ?Gbinding (no ?S)
>
> |
>
> -86.3579
>
> |
>
> -30.8353
>
> |
>
> In your results, the binding of ras_raf complex is favored although this is not real binding free energy.
>
> |
> | | | |
> | | |
>
>
>
>
> While I have done a test for choosing different parameters in amber16 with 5 frames as following:
>
> Table 2?The average binding free energy with entropy effect of 5 frames from amber16 by choose different parameters (kcal/mol?
>
> |
>
>
>
> |
>
> Inp=0
>
> |
>
> Inp=1
>
> |
>
> Inp=2
>
> |
> |
>
>
>
> |
>
> Radiopt=0
>
> |
>
> Radiopt=1
>
> |
>
> Radiopt=0
>
> |
>
> Radiopt=0
>
> |
>
> Radiopt=1
>
> |
> |
>
> ?Emm
>
> |
>
> -1060.0425
>
> |
>
> -1060.0425
>
> |
>
> -1060.0425
>
> |
>
> -1060.0425
>
> |
>
> -1060.0425
>
> |
> |
>
> ?EPB
>
> |
>
> 969.7617
>
> |
>
> 978.3053
>
> |
>
> 969.7617
>
> |
>
> 969.7617
>
> |
>
> 978.3053
>
> |
> |
>
> ?ENpolar
>
> |
>
> --
>
> |
>
> --
>
> |
>
> -7.5509
>
> |
>
> -51.5872
>
> |
>
> -51.5872
>
> |
> |
>
> ?Edisper
>
> |
>
> --
>
> |
>
> --
>
> |
>
> --
>
> |
>
> 107.2185
>
> |
>
> 102.4891
>
> |
> |
>
> ?Sentropy
>
> |
>
> -42.0761
>
> |
>
> -42.0761
>
> |
>
> -42.0761
>
> |
>
> -42.0761
>
> |
>
> -42.0761
>
> |
> |
>
> ?Gbinding (no ?S)
>
> |
>
> -90.2807
>
> |
>
> -81.7371
>
> |
>
> -97.8316
>
> |
>
> -34.6494
>
> |
>
> -30.8353
>
> |
> |
>
> ?Gbinding (?S)
>
> |
>
> -48.2047
>
> |
>
> -39.662
>
> |
>
> -55.7555
>
> |
>
> 7.4267
>
> |
>
> 11.2409
>
> |
>
> Actually, we can see that the binding eneries with entropy effect are differents with regulating the parameters.
>
> The default parameter result of amber16 is 11.2409 kcal/mol withinp =2 and radiopt=1,while the binding free energy is -55.7555 kcal/mol with inp =1 and radiopt=0. Which result i can trusted and used ?
>
> So I am very confused of this default parameter result with taking depersion energy into account. And what is the favor of parameter of inp =2 comparing to inp=1.
>
> I really hope to hear from you as soon as possible!
> Best Wishes
>
>
>
> Fangjia Fu
>
> ------------------------------
>
> Message: 2
> Date: Mon, 18 Mar 2019 00:48:00 -0400
> From: Feng Pan <fpan3.ncsu.edu>
> Subject: Re: [AMBER] Amber18 STSM
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAHZ=aZcdZBmZF6cukBY2=0UpLDk0xU2=WmcBZD-yrC7b9kKjMg.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi, Yao Li
>
> You cannot run with just ONE image, the string method only applies when you
> use multiple images.
>
> Feng
>
> On Sat, Mar 16, 2019 at 9:39 AM ?? <liyao17.mails.tsinghua.edu.cn> wrote:
>
>> Dear Amber users,
>>
>>
>> I'm running Swarms-of-trajectories String Method in Amber 18, and these
>> are a pair of example of my input files and cv files:
>>
>>
>> mdin.001:
>> &cntrl
>> imin=0, ntx=1, irest=0, ntxo=1, ntc=2, ntf=2, nstlim=10000,
>> ntt=3, gamma_ln=2.0, temp0=300.0, ntpr=10, ntwr=10, ntwx=10,
>> dt=0.002, ig=-1, ntb=1,ntr=0, cut=10.0, ioutfm=1,
>> iwrap=1,infe=1,
>> /
>>
>>
>> &stsm
>> image = 1
>> repeats = 20
>> equilibration = 980
>> release = 20
>> smoothing = 0.06
>> report_centers = 'ALL'
>>
>>
>> output_file = 'stsm.001.txt'
>> output_freq = 10
>> cv_file = 'cv.1'
>> /
>> cv.1:
>> &colvar
>> cv_type = 'TORSION'
>> cv_ni = 4, cv_i = 5653, 5639, 5620, 5551
>> anchor_position = 0.5235
>> anchor_strength = 20.0
>> /
>>
>>
>> &colvar
>> cv_type = 'TORSION'
>> cv_ni = 4, cv_i = 5541, 5649, 5653, 3386
>> anchor_position = 1.5705
>> anchor_strength = 20.0
>> /
>>
>>
>> The command is: nohup /software/amber18/bin/pmemd.cuda -O -i mdin.001 -p
>> new_mono.prmtop -c inpcrd.001 -o test1.out -x test1.nc -r test1.restrt
>> -inf test1.info & . And it came out the following error:
>>
>>
>> Program received signal SIGFPE: Floating-point exception - erroneous
>> arithmetic operation.
>>
>>
>> Backtrace for this error:
>> #0 0x7FCB8B688E08
>> #1 0x7FCB8B687F90
>> #2 0x7FCB8AA374AF
>> #3 0x6AE5A1 in __nfe_stsm_mod_MOD_on_pmemd_init
>> #4 0x677A84 in __nfe_setup_mod_MOD_on_pmemd_init
>> #5 0x4B56DB in MAIN__ at pmemd.F90:?
>>
>>
>> When I set infe to 0 to turn stsm down, it works well. I couldn't figure
>> out what the problem is. Have you met similar situations before? What
>> should I do about this?
>>
>>
>> Thank you!
>>
>>
>> Best,
>> Yao Li
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
> Feng Pan
> PostDoc
> North Carolina State University
> Department of Physics
> Email: fpan3.ncsu.edu
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 18 Mar 2019 08:36:08 +0100
> From: Ruth Helena Tichauer <rhtichau.laas.fr>
> Subject: Re: [AMBER] velocities from and velocityautocorr
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <3891D916-956D-4007-AE5F-090C330D7B3C.laas.fr>
> Content-Type: text/plain; charset=utf-8
>
> Dear Daniel,
>
> Indeed, employing the two masks results in the MSD(t) being calculated for 1 or 2 water molecules at the time.. So, as you pointed out, the issue might be the small amount of water molecules considered for the diffusion calculation.
>
> Thank you again for your detailed reply,
>
> Sincerely yours,
>
> Ruth
>
>> On 15 Mar 2019, at 20:30, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>> Hi,
>>
>> On Fri, Mar 15, 2019 at 10:08 AM Ruth Helena Tichauer <rhtichau.laas.fr <mailto:rhtichau.laas.fr>> wrote:
>>>
>>> However, I get the MSD(t) plot here attached (MSD in the xyz dimension against time). As it is not a linear plot, I don?t know how to infer from it the diffusion coefficient.. Considering an initial linear portion of the plot does not seem like an available option here..
>>
>> There might not be enough data going into the diffusion calculation.
>> In general a lot of averaging is needed (over time and molecules) to
>> get reliable translational diffusion estimates.
>>
>>>
>>> it seems that the distances keyword, provided to the stfcdiffuion command has no effect . Indeed, while processing I get the following message:
>>
>> Indeed, looking at the code it seems that 'distances' is disabled if
>> 'mask2' has been specified. I'm not sure why (I'm not the original
>> author of the code) but it would take some re-coding to get it to
>> work. Feel free to make a feature request on GitHub, but unfortunately
>> the next few months are going to be very busy for me so I might not
>> get to it for a while.
>>
>> -Dan
>>
>>>
>>> CPPTRAJ: Trajectory Analysis. V17.00
>>> ___ ___ ___ ___
>>> | \/ | \/ | \/ |
>>> _|_/\_|_/\_|_/\_|_
>>>
>>> | Date/time: 03/14/19 16:52:08
>>> | Available memory: 246.294 MB
>>>
>>> INPUT: Reading input from 'natmm_msd-dis.in'
>>> [parm ../../../native2-0.parm]
>>> Reading '../../../native2-0.parm' as Amber Topology
>>> Radius Set: modified Bondi radii (mbondi)
>>> This Amber topology does not include atomic numbers.
>>> Assigning elements from atom masses/names.
>>> No SCEE section: setting Amber default (1.2)
>>> No SCNB section: setting Amber default (2.0)
>>> [trajin ../../../traj_nc-autoimaged/nat2-0_md1-ai.nc]
>>> Reading '../../../traj_nc-autoimaged/nat2-0_md1-ai.nc' as Amber NetCDF
>>> ...
>>> [trajin ../../../traj_nc-autoimaged/nat2-0_md10-ai.nc]
>>> Reading '../../../traj_nc-autoimaged/nat2-0_md10-ai.nc' as Amber NetCDF
>>> [stfcdiffusion mask :WAT.O&!(:196-197) time 1.0 mask2 :GTP.PG lower 0.01 upper 5.0 xyz distances out natmm_msd-dis.out nwout natmm_nw-dis.out avout natmm_av-dis.out ]
>>> DIFFUSION (STFC): Calculating diffusion in the xyz directions
>>> Mask 1 expression: :WAT.O&!(:196-197)
>>> Atoms in mask 2 (:GTP.PG) in the range 0.010 to 5.000 Angstrom will be used
>>> Distances will be imaged.
>>> Only the average results will be written to natmm_msd-dis.out
>>> The number of atoms in the shell will be written to natmm_nw-dis.out
>>> <dr^2> will be written to natmm_av-dis.out
>>> The time step between frames is 1.000 ps.
>>> ---------- RUN BEGIN -------------------------------------------------
>>>
>>> and so I don?t know how correct the obtained plot is (red line):
>>>
>>>
>>>
>>> As the version I used was the following:
>>>
>>> python /Users/administrateur/amber16/update_amber --version
>>> Version is reported as <version>.<patches applied>
>>>
>>> AmberTools version 17.09
>>> Amber version 16.14
>>>
>>> I?ve tried to upgrade AmberTools but didn?t get anything:
>>>
>>> python /Users/administrateur/amber16/update_amber --update-to AmberTools/18
>>> Preparing to apply specific updates... please wait.
>>>
>>> So I've just updated to latest version that now is:
>>>
>>> python /Users/administrateur/amber16/update_amber --version
>>> Version is reported as <version>.<patches applied>
>>>
>>> AmberTools version 17.10
>>> Amber version 16.15
>>>
>>> Nevertheless, I still get the exact same results as with the previous version i.e. exact same plots for both input files and same information about imaging distances despite the distances keyword provided when analysing autoimaged trajectories.
>>>
>>> Thanking you and anyone for any help on any of these issues.
>>>
>>> Sincerely yours,
>>>
>>> Ruth
>>>
>>>> On 13 Mar 2019, at 21:56, Ruth Helena Tichauer <rhtichau.laas.fr> wrote:
>>>>
>>>> Dear Daniel,
>>>>
>>>> Thank you so much for providing me detailed insight into this matter.
>>>> I?ll carefully check all your suggestions on the manual and I?ll come back to you if I have any further inquiries after trying the analysis you propose.
>>>>
>>>> All the best,
>>>>
>>>> Ruth
>>>>
>>>>> On 13 Mar 2019, at 18:17, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> On Wed, Mar 13, 2019 at 12:07 PM Ruth Helena Tichauer <rhtichau.laas.fr> wrote:
>>>>>> I wish to compute the velocity autocorrelation function (VACf) of water molecules within the cavity of a protein-ligand complex. I wish to use the usevelocity keyword as in http://archive.ambermd.org/201605/0236.html <http://archive.ambermd.org/201605/0236.html> but I haven?t saved any velocity information while running the calculations.. Is there a straightforward manner to re-calculate these velocities from the .nc trajectory file (using cpptraj perhaps)? FYI the trajectories I wish to analyse are 10ns long such that frames were recorded every 1 ps (I wonder if this sampling is enough).
>>>>>
>>>>> Unfortunately that frequency isn't nearly enough for calculating the
>>>>> velocity autocorrelation function (which decays more on the order of
>>>>> fs). I usually record velocities every 10 fs or so when calculationg
>>>>> VAC. You're better off using the 'diffusion' command and good ole
>>>>> Einstein relation.
>>>>>
>>>>>>
>>>>>> Aside, when reading the manual concerning the velocityautocorr analysis, it is not clear to me what the maxlag is.. Neither what tstep refers to: is it the time difference for computing the autocorrelation i.e the tau in <v(t)v(t+tau)>?
>>>>>
>>>>> The 'maxlag' is the maximum lag you want to calculate the VAC function
>>>>> for (tau in your equation). This is in general something to keep in
>>>>> mind when calculation any autocorrelation function - as your lag
>>>>> increases, the number of data points that go into calculating the
>>>>> function at that point decreases and the function becomes "noisy". The
>>>>> 'tstep' is just the timestep between frames in ps.
>>>>>
>>>>>>
>>>>>> As the VACf is computed for a mask of atoms, and as I wish to get an estimate of the diffusion coefficient of water molecules when they are in the protein cavity (to see if this value is different from the bulk), should I select water molecules within the cavity only (I guess so)? If yes, as they exchange during the simulated time with water molecules from the bulk, should I account for the portions of the trajectory during which they are inside the cavity only (I also suppose yes so but I rather ask)?
>>>>>
>>>>> This is a much trickier problem - in this case I'd recommend using the
>>>>> 'stfcdiffusion' command, which can calculate diffusion for atoms
>>>>> within a certain distance (defined by 'upper' and 'lower') from atoms
>>>>> selected by a mask ('mask2') - see the manual for more details.
>>>>>
>>>>> -Dan
>>>>>
>>>>>>
>>>>>> Any help concerning any of the previous points will be much appreciated.
>>>>>>
>>>>>> Thanking you in advance,
>>>>>>
>>>>>> Sincerely,
>>>>>>
>>>>>> Ruth
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>> _______________________________________________
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>>> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 18 Mar 2019 11:41:46 +0100
> From: Tr?g, Johannes <johannes.traeg.fau.de>
> Subject: Re: [AMBER] gaff2 parameters of c3-c3-os-c3
> To: David Case <david.case.rutgers.edu>, AMBER Mailing List
> <amber.ambermd.org>
> Message-ID: <49d74192263a7d0562f5e7d3904db818.fau.de>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Am 2019-03-15 20:20, schrieb David Case:
>> On Fri, Mar 15, 2019, Tr?g, Johannes wrote:
>>>
>>> I have a question regarding the assignment of GAFF2 parameters
>>> (gaff2.dat, Version 2.1, April 2016) to the dihedral angle
>>> c3-c3-os-c3.
>>>
>>> For this dihedral angle, the gaff2.dat file lists the following lines:
>>>
>>> X -c3-os-X 3 1.150 0.000 3.000
>>> JCC,7,(1986),230
>>>
>>> c3-os-c3-c3 1 0.240 0.000 -3 p29 GA
>>> c3-os-c3-c3 1 0.160 0.000 2 p29 GA
>>>
>>> c3-c3-os-c3 1 0.910 0.000 -3
>>> c3-c3-os-c3 1 1.000 0.000 -2
>>> c3-c3-os-c3 1 0.000 0.000 1
>>>
>>> Of course the fist line has to be omitted, since there are explicit
>>> entries for c3-c3-os-c3/c3-os-c3-c3. However, the .frcmod file
>>> prepared
>>> by parmchk2 lists the following lines:
>>
>> Can you say exactly what arguments you gave to parmchk2 to get this
>> result? Did you include the "-s 2" option? (cc-ing to Junmei for
>> comments as well.)
>>
> I used tha following command: parmchk2 -i ff.mol2 -f mol2 -o ff.frcmod
> -s 2 -a Y
>
>
>>>
>>> c3-c3-os-c3 1 0.240 0.000 -3.000
>>> c3-c3-os-c3 1 0.160 0.000 2.000
>>> c3-c3-os-c3 1 1.000 0.000 -2.000
>>> c3-c3-os-c3 1 0.000 0.000 1.000
>>>
>>> Finally, the .prmtop file prepared by leap contains only the values of
>>> theses lines:
>>>
>>> c3-c3-os-c3 1 0.240 0.000 -3.000
>>> c3-c3-os-c3 1 0.160 0.000 2.000
>>> c3-c3-os-c3 1 0.000 0.000 1.000
>>>
>>> Why is the line (1/0.910/0.000/2) missing in .frcmod? How (and why) do
>>> antechamber/leap choose the final values for the .prmtop file and not
>>> the lines (1/0.910/0.000/-3 1/1.000/0.000/-2) instead?
>>>
>>
>> ...dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 18 Mar 2019 11:20:51 +0000 (UTC)
> From: david stephen <davidstephen_dav.yahoo.co.in>
> Subject: [AMBER] Installation Problem
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <1965151538.6449137.1552908051492.mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> Respected Professor,
> Thanks for your kind support so far provided to me and my research team.
> Now i am installing whole amber16 package to my new workstation having CENTOS 6 (64 bit). I got the following error which i can not resolved,
> I presumed the problem lies in the version of Python. The in-built centos 6 got python 2.6, but AMBER needs version atleast 2.7. I installed python 2.7, still the problem persist, i copied the error message when configurin the amber16...
> ./configure2: line 947: cd: /opt/amber16/bin: No such file or directoryUsing the AmberTools miniconda installation in /opt/amber16/minicondaversion ./configure2: line 64: /opt/amber16/bin/amber.python: No such file or directory
> Obtaining the gnu compiler suite versions, e.g.:? ? ?gcc -vThe C version is 4.4.7The Fortran version is 4.4.7
> Testing the gcc compiler:? ? ?gcc -fPIC? -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE? -o testp testp.cOK
> Testing the g++ compiler:? ? ?g++ -fPIC? -o testp testp.cppIn file included from testp.cpp:1:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio:43:28: error: bits/? ? ? ? ? ? ? ? ? ? ? ? ?c++config.h: No such file or directoryIn file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstd? ? ? ? ? ? ? ? ? ? ? ? ?io:44,? ? ? ? ? ? ? ? ?from testp.cpp:1:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef:49: error: expecte? ? ? ? ? ? ? ? ? ? ? ? ?d constructor, destructor, or type conversion before ?(? tokenIn file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstd? ? ? ? ? ? ? ? ? ? ? ? ?io:45,? ? ? ? ? ? ? ? ?from testp.cpp:1:/usr/include/stdio.h:30: error: expected constructor, destructor, or type conversion before ?ex? ? ? ? ? ? ? ? ? ? ? ? ?tern?./configure2: line 2288: ./testp: No such file or directoryError: Unable to compile a C program using g++ -fPIC? ? ? ?Please check your compile
r settings or configure flags.Configure failed due to the errors above!
>
> Kindly do the needful help
>
> Thanking you?Sincerely?Dr. A. David Stephen?Dept. of Physics?SSIET - Coimbatore,Tamilnadu, INDIA
>
> ------------------------------
>
> Message: 6
> Date: Mon, 18 Mar 2019 05:00:04 -0700
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] Installation Problem
> To: amber.ambermd.org
> Message-ID: <18078d59-ff85-e46d-b101-22c311c9a474.cgl.ucsf.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> It seems the problem is your g++ installation or another setup step:
>
> Unable to compile a C program using g++
>
> Bill
>
>
> On 3/18/19 4:20 AM, david stephen wrote:
>> Respected Professor,
>> Thanks for your kind support so far provided to me and my research team.
>> Now i am installing whole amber16 package to my new workstation having CENTOS 6 (64 bit). I got the following error which i can not resolved,
>> I presumed the problem lies in the version of Python. The in-built centos 6 got python 2.6, but AMBER needs version atleast 2.7. I installed python 2.7, still the problem persist, i copied the error message when configurin the amber16...
>> ./configure2: line 947: cd: /opt/amber16/bin: No such file or directoryUsing the AmberTools miniconda installation in /opt/amber16/minicondaversion ./configure2: line 64: /opt/amber16/bin/amber.python: No such file or directory
>> Obtaining the gnu compiler suite versions, e.g.:? ? ?gcc -vThe C version is 4.4.7The Fortran version is 4.4.7
>> Testing the gcc compiler:? ? ?gcc -fPIC? -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE? -o testp testp.cOK
>> Testing the g++ compiler:? ? ?g++ -fPIC? -o testp testp.cppIn file included from testp.cpp:1:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio:43:28: error: bits/? ? ? ? ? ? ? ? ? ? ? ? ?c++config.h: No such file or directoryIn file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstd? ? ? ? ? ? ? ? ? ? ? ? ?io:44,? ? ? ? ? ? ? ? ?from testp.cpp:1:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef:49: error: expecte? ? ? ? ? ? ? ? ? ? ? ? ?d constructor, destructor, or type conversion before ?(? tokenIn file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstd? ? ? ? ? ? ? ? ? ? ? ? ?io:45,? ? ? ? ? ? ? ? ?from testp.cpp:1:/usr/include/stdio.h:30: error: expected constructor, destructor, or type conversion before ?ex? ? ? ? ? ? ? ? ? ? ? ? ?tern?./configure2: line 2288: ./testp: No such file or directoryError: Unable to compile a C program using g++ -fPIC? ? ? ?Please check your compil
er settings or configure flags.Configure failed due to the errors above!
>>
>> Kindly do the needful help
>>
>> Thanking you?Sincerely?Dr. A. David Stephen?Dept. of Physics?SSIET - Coimbatore,Tamilnadu, INDIA
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> ------------------------------
>
> Message: 7
> Date: Mon, 18 Mar 2019 09:08:11 -0300
> From: Gerardo Zerbetto De Palma <g.zerbetto.gmail.com>
> Subject: Re: [AMBER] Installation Problem
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAOMpsaUmFU0cDuxVb2ytyU-=n7RbrpZ7hPygE9wK3CJcj4LHvg.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Try to update gcc, g++ and gfortran to 4.8 version.
> Regards!
> Gera
>
> El lun., 18 de mar. de 2019 09:00, Bill Ross <ross.cgl.ucsf.edu> escribi?:
>
>> It seems the problem is your g++ installation or another setup step:
>>
>> Unable to compile a C program using g++
>>
>> Bill
>>
>>
>> On 3/18/19 4:20 AM, david stephen wrote:
>>> Respected Professor,
>>> Thanks for your kind support so far provided to me and my research team.
>>> Now i am installing whole amber16 package to my new workstation having
>> CENTOS 6 (64 bit). I got the following error which i can not resolved,
>>> I presumed the problem lies in the version of Python. The in-built
>> centos 6 got python 2.6, but AMBER needs version atleast 2.7. I installed
>> python 2.7, still the problem persist, i copied the error message when
>> configurin the amber16...
>>> ./configure2: line 947: cd: /opt/amber16/bin: No such file or
>> directoryUsing the AmberTools miniconda installation in
>> /opt/amber16/minicondaversion ./configure2: line 64:
>> /opt/amber16/bin/amber.python: No such file or directory
>>> Obtaining the gnu compiler suite versions, e.g.: gcc -vThe C version
>> is 4.4.7The Fortran version is 4.4.7
>>> Testing the gcc compiler: gcc -fPIC -D_FILE_OFFSET_BITS=64
>> -D_LARGEFILE_SOURCE -o testp testp.cOK
>>> Testing the g++ compiler: g++ -fPIC -o testp testp.cppIn file
>> included from
>> testp.cpp:1:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio:43:28:
>> error: bits/ c++config.h: No such file or
>> directoryIn file included from
>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstd
>> io:44, from
>> testp.cpp:1:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef:49:
>> error: expecte d constructor, destructor, or type
>> conversion before ?(? tokenIn file included from
>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstd
>> io:45, from
>> testp.cpp:1:/usr/include/stdio.h:30: error: expected constructor,
>> destructor, or type conversion before ?ex
>> tern?./configure2: line 2288: ./testp: No such file or directoryError:
>> Unable to compile a C program using g++ -fPIC Please check your
>> compiler settings or configure flags.Configure failed due to the errors
>> above!
>>>
>>> Kindly do the needful help
>>>
>>> Thanking you Sincerely Dr. A. David Stephen Dept. of Physics SSIET -
>> Coimbatore,Tamilnadu, INDIA
>>> _______________________________________________
>>> 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: 8
> Date: Mon, 18 Mar 2019 05:18:51 -0700
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] Installation Problem
> To: amber.ambermd.org
> Message-ID: <7aefb438-c4fb-f719-ec2f-98f42b5d142a.cgl.ucsf.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Also, maybe it's time for AmberTools 18?
>
> http://ambermd.org/AmberTools.php
>
> On 3/18/19 5:00 AM, Bill Ross wrote:
>> It seems the problem is your g++ installation or another setup step:
>>
>> Unable to compile a C program using g++
>>
>> Bill
>>
>>
>> On 3/18/19 4:20 AM, david stephen wrote:
>>> Respected Professor,
>>> Thanks for your kind support so far provided to me and my research team.
>>> Now i am installing whole amber16 package to my new workstation having CENTOS 6 (64 bit). I got the following error which i can not resolved,
>>> I presumed the problem lies in the version of Python. The in-built centos 6 got python 2.6, but AMBER needs version atleast 2.7. I installed python 2.7, still the problem persist, i copied the error message when configurin the amber16...
>>> ./configure2: line 947: cd: /opt/amber16/bin: No such file or directoryUsing the AmberTools miniconda installation in /opt/amber16/minicondaversion ./configure2: line 64: /opt/amber16/bin/amber.python: No such file or directory
>>> Obtaining the gnu compiler suite versions, e.g.:? ? ?gcc -vThe C version is 4.4.7The Fortran version is 4.4.7
>>> Testing the gcc compiler:? ? ?gcc -fPIC? -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE? -o testp testp.cOK
>>> Testing the g++ compiler:? ? ?g++ -fPIC? -o testp testp.cppIn file included from testp.cpp:1:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio:43:28: error: bits/? ? ? ? ? ? ? ? ? ? ? ? ?c++config.h: No such file or directoryIn file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstd? ? ? ? ? ? ? ? ? ? ? ? ?io:44,? ? ? ? ? ? ? ? ?from testp.cpp:1:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef:49: error: expecte? ? ? ? ? ? ? ? ? ? ? ? ?d constructor, destructor, or type conversion before ?(? tokenIn file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstd? ? ? ? ? ? ? ? ? ? ? ? ?io:45,? ? ? ? ? ? ? ? ?from testp.cpp:1:/usr/include/stdio.h:30: error: expected constructor, destructor, or type conversion before ?ex? ? ? ? ? ? ? ? ? ? ? ? ?tern?./configure2: line 2288: ./testp: No such file or directoryError: Unable to compile a C program using g++ -fPIC? ? ? ?Please check your compi
ler settings or configure flags.Configure failed due to the errors above!
>>>
>>> Kindly do the needful help
>>>
>>> Thanking you?Sincerely?Dr. A. David Stephen?Dept. of Physics?SSIET - Coimbatore,Tamilnadu, INDIA
>>> _______________________________________________
>>> 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: 9
> Date: Mon, 18 Mar 2019 20:41:16 +0800 (CST)
> From: bjyx20090941 <bjyx20090941.163.com>
> Subject: [AMBER] pdb file with 4 atoms coordinates of water molecules
> with TIP4PFB model
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID: <757aa168.16a69.16990d20596.Coremail.bjyx20090941.163.com>
> Content-Type: text/plain; charset=GBK
>
> Dear amber:
> I used TIP4PFB force field to run explicit water in MD simulation with Amber16. We all konw that the TIP4PFB as same as TIP4P model has every 4 atoms coordinates of H2O in water.mdcrd file. While when I used cpptraj module generating: trajin *.mdcrd 1 1 1 trajout *.pdb
> I found the generating *.pdb file just have 3 atoms coordinates like O H1 H2, which is differ from the TIP4PFB model file with O H1 H2 EP 4 atoms coordinates. But I want the pdb file with4 atoms coordinates. So is there any command i do not kown for this in capptraj module, just not use python or fortran by myself.
>
>
> I am hope hear from you!
>
>
> Best Wishes
>
>
> Fangjia Fu
>
> ------------------------------
>
> Message: 10
> Date: Mon, 18 Mar 2019 08:49:47 -0400
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] pdb file with 4 atoms coordinates of water
> molecules with TIP4PFB model
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qOYQ8stBkGBC3KFy9n_V5PzgczXGG_N_EszPET_aHSE-sg.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> You need to use the 'include_ep' keyword when writing your PDB file, e.g.
>
> trajin mytraj.nc
> trajout mypdb.pdb include_ep
>
> -Dan
>
> On Mon, Mar 18, 2019 at 8:41 AM bjyx20090941 <bjyx20090941.163.com> wrote:
>>
>> Dear amber:
>> I used TIP4PFB force field to run explicit water in MD simulation with Amber16. We all konw that the TIP4PFB as same as TIP4P model has every 4 atoms coordinates of H2O in water.mdcrd file. While when I used cpptraj module generating: trajin *.mdcrd 1 1 1 trajout *.pdb
>> I found the generating *.pdb file just have 3 atoms coordinates like O H1 H2, which is differ from the TIP4PFB model file with O H1 H2 EP 4 atoms coordinates. But I want the pdb file with4 atoms coordinates. So is there any command i do not kown for this in capptraj module, just not use python or fortran by myself.
>>
>>
>> I am hope hear from you!
>>
>>
>> Best Wishes
>>
>>
>> Fangjia Fu
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 11
> Date: Tue, 19 Mar 2019 00:20:23 +0530
> From: Bharat Manna <bharatmanna.gmail.com>
> Subject: [AMBER] Assigning protonation states manually to the amino vs
> CpH MD simulation
> To: amber.ambermd.org
> Message-ID:
> <CAK7c+Nj51Ah764VBV7NzTDwCLCbdDmA1NiDTjn=biTZsPn+NeA.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear AMBER Users,
>
> If I assign the protonation states of the amino acid residues manually in
> the PDB file (e.g. at pH 8.0, HIS -> HIP, LYS -> LYS etc.) while generating
> the topology in Leap, and perform conventional MD simulation of the
> protein, will it be similar to Constant pH MD simulation? To be more
> precise, will the results obtained from the simulation be comparable to the
> behaviour of the protein at that particular pH?
>
> Thanks,
> B Manna
> PhD Scholar
>
>
> ------------------------------
>
> Message: 12
> Date: Mon, 18 Mar 2019 10:05:15 -0400
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Subject: Re: [AMBER] Assigning protonation states manually to the
> amino vs CpH MD simulation
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAGk3s-RP_hvhqzG+cY5UoUq0F2EhJ4V-jHwzxP74pv3_Nws6aw.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> They will if your protonation states are known and not likely to change for
> the states sampled during md.
>
> I would be surprised if HIP was appropriate for pH 8. Maybe, but not
> without a pKa shift.
>
> On Mon, Mar 18, 2019, 9:18 AM Bharat Manna <bharatmanna.gmail.com> wrote:
>
>> Dear AMBER Users,
>>
>> If I assign the protonation states of the amino acid residues manually in
>> the PDB file (e.g. at pH 8.0, HIS -> HIP, LYS -> LYS etc.) while generating
>> the topology in Leap, and perform conventional MD simulation of the
>> protein, will it be similar to Constant pH MD simulation? To be more
>> precise, will the results obtained from the simulation be comparable to the
>> behaviour of the protein at that particular pH?
>>
>> Thanks,
>> B Manna
>> PhD Scholar
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> ------------------------------
>
> Message: 13
> Date: Mon, 18 Mar 2019 13:12:37 -0400
> From: Jason Imamoto <jimamoto.mail.usciences.edu>
> Subject: [AMBER] Nastruct vs 3DNA
> To: amber.ambermd.org
> Message-ID: <5F2C7EEF-5728-4163-A644-2D1CB4879E5B.mail.usciences.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Hello Users,
>
> I had a question about the nastruct command compared to x3dna. The current nastruct does not seem capable of identifying non-canonical base-pairs. Are there variables that can be changed for it to recognize non-canonical base-pairs to acquire base and base-step parameters? I know that x3dna is capable of producing those parameters and since nastruct is based on x3dna, I would think it is capable of doing the same analysis.
>
> Thank you for your time and help.
>
> Jason M. Imamoto
> Doctoral Candidate
> Department of Chemistry and Biochemistry
> GH 302
> University of the Sciences in Philadelphia
> 600 S 43rd St. Philadelphia, PA 19104
>
> Email: jimamoto.mail.usciences.edu
>
>
>
>
> ------------------------------
>
> Message: 14
> Date: Mon, 18 Mar 2019 13:37:04 -0400
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] Nastruct vs 3DNA
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qObjxJZ81HJzK8QZRogbnAEsSrRkUN4yZj7LTWV9+n6izg.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> Just to clarify, what version of cpptraj are you referring to exactly
> (i.e. what are the results of 'cpptraj --version' and 'cpptraj
> --internal-version')?
>
> -Dan
>
> On Mon, Mar 18, 2019 at 1:12 PM Jason Imamoto
> <jimamoto.mail.usciences.edu> wrote:
>>
>> Hello Users,
>>
>> I had a question about the nastruct command compared to x3dna. The current nastruct does not seem capable of identifying non-canonical base-pairs. Are there variables that can be changed for it to recognize non-canonical base-pairs to acquire base and base-step parameters? I know that x3dna is capable of producing those parameters and since nastruct is based on x3dna, I would think it is capable of doing the same analysis.
>>
>> Thank you for your time and help.
>>
>> Jason M. Imamoto
>> Doctoral Candidate
>> Department of Chemistry and Biochemistry
>> GH 302
>> University of the Sciences in Philadelphia
>> 600 S 43rd St. Philadelphia, PA 19104
>>
>> Email: jimamoto.mail.usciences.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
>
>
> End of AMBER Digest, Vol 2589, Issue 1
> **************************************
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 18 2019 - 12:30:02 PDT
