Re: [gmx-users] energy minimization
Dear Justin
But I copied & pasted topolgen and perl5 folders in the working directory. and
faced the mentioned error.
Can't open perl script "topolgen.pl": No such file or directory
I dont know how I should figure out this problem.
Which one of all-atom force fields will you choose to run a simulation on a
complex with small molecule, if you want to calculate binding energy using
G_MMPBSA ?I really need your guidance .
best
Farial
On Saturday, July 14, 2018, 6:35:27 PM GMT+4:30, Justin Lemkul
wrote:
On 7/14/18 5:03 AM, farial tavakoli wrote:
>
> Dear justin
>
> I am trying to run a simulation on my complex which has small molecule as a
> ligand , using OPLSAA ff. so I downloaded the topolgen-1.1.tgz and then
> installed perl script on linux. then typed "perl -v" to check if it is
> installed. the perl 5.20.1 was installed.
> but when I typed " perl topolgen.pl -f input.pdb -o output.top [-type
> itp/top] " command to generate ligand topology , faced with this error:
> Can't open perl script "topolgen.pl": No such file or directory
> Infact I am new user in generation topology for small molecules using OPLSAA
> ff. Would you please help me to figure out this problem?
"No such file or directory" means the file isn't in the working
directory. This is a generic error message from your shell and nothing
specific about the script itself.
-Justin
>
> Farial
> best
> On Tuesday, February 20, 2018, 10:24:49 PM GMT+3:30, Justin Lemkul
> wrote:
>
>
>
> On 2/20/18 12:52 PM, farial tavakoli wrote:
>> blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
>>#715FFA solid !important; padding-left:1ex !important; background-color:white
>>!important; } Dear Justin
>> Thank you for the reply
>> You meant , to tweak the emtol doesn't have noticable affects on the
>> conformational enssemble generated by MD?
>>
> Precisely what I said, yes.
>
> -Justin
>
>> Sent from Yahoo Mail for iPhone
>>
>>
>> On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul
>> wrote:
>>
>>
>>
>> On 2/20/18 4:52 AM, farial tavakoli wrote:
>>> Dear GMX users
>>> I used CHARMM36 all atom force field to generate .top and .gro files for my
>>> complex composed of a receptor protein and a ligand with 2 phosphotyrosine
>>> residues, then ran a md simulation on it and then used g_mmpbsa to
>>> calculate the binding free energy by pdies ( 2 and 4) but got + 426 and
>>> +527 kjol/mol, respectively. While, I calculated binding energy before for
>>> many other complexes without any phosphate groups using OPLS all atom force
>>> field and pdie = 2 and obtained minus energy. But this time , I dont know
>>> why I got positive binding energy? Is it because of charmm36 all atom force
>>> field , the phosphate groups or it is needed to be energy minimized under
>>> more restriction situations?
>>> I am checking different factors to understand its reason, so I wanted to
>>> know , would it be ok if I energy minimize the complex with more
>>> restriction situations ? for example by specifying emtol under 1000
>>> kj/mol/nm , like 800 ? I think the positive binding energy might be because
>>> of the complex didnt minimized well. however I checked the em.log file and
>>> saw it was minimized well:
>>>
>>> Steepest Descents converged to Fmax < 1000 in 241 steps
>>> Potential Energy = -6.5047744e+05
>>> Maximum force = 9.8285083e+02 on atom 3335
>>> Norm of force = 3.6905827e+01
>>> Is there anyone can advice me in energy minimization with emtol 800?
>> The purpose of energy minimization is to establish a reasonable starting
>> point for your simulation. Tweaks to emtol will have little to no
>> noticeable bearing on the conformational ensemble generated by MD.
>>
>> -Justin
>>
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==
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[gmx-users] gmx spatial producing negative isodensities.
Dear all, I have been attempting to obtain SDFs using gmx spatial however with the results of getting negative isodensities. The trajectory contains 25000 frames, and ~1 atoms. Running gmx spacial with: gmx spatial -s mol_packed.gro -f mol.xtc -bin 0.1 and choosing the co-solute of interest to generate the SDF for and choosing the system for group to output coords, yielded the following: Counts per frame in all 160380 cubes divided by -7.881814e-02 Normalized data: average 1.00e+00, min -0.00e+00, max -2.103577e+00 This test was conducted on 2 different machines 1 using gromacs version 2018.2 and second 2016.3. Further we found that conducting the very same analysis however using a bin size of 0.14 yields reasonable results, here meaning postive isodensities. So my questions are: Has this behaviour been observed before? i.e. is this a bug? Am I using the gmx spatial wrong? Regards, Stefan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trjcat -settime
On 7/14/18 12:28 PM, Atila Petrosian wrote: Dear Justin, "This is addressed in basic tutorials if you're not familiar with it" I used mdp files from your web page (GROMACS Tutorials): http://www.mdtutorials.com/gmx/lysozyme/06_equil.html http://www.mdtutorials.com/gmx/lysozyme/07_equil2.html Have these files problem? They don't have problems, nor does the approach taken there. I'm making guesses based on incomplete information. You haven't shown any sequences of commands, proof that you have the coordinates in each .tpr that you think you do, etc. I'm trying to rationalize weird data. Maybe you just used npt.tpr as your reference for the RMSD calculation, which is what makes the most sense, but again, providing your actual commands for everything would save a lot of time. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trjcat -settime
On 7/14/18 12:06 PM, Atila Petrosian wrote: Dear Justin, I used following: continuation = no, in nvt.mdp (first md run, 500 ps) continuation = yes, in npt.mdp (second md run, 1000 ps). Is my manner wrong? That just means the constraints won't be re-solved before the first step of the second simulation. You need to pass the appropriate coordinate and checkpoint files to continue from the end point of the previous simulation. This is addressed in basic tutorials if you're not familiar with it. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] trjcat -settime
Dear Justin, I used following: continuation = no, in nvt.mdp (first md run, 500 ps) continuation = yes, in npt.mdp (second md run, 1000 ps). Is my manner wrong? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trjcat -settime
On 7/14/18 10:54 AM, Atila Petrosian wrote: Hi Justin, Thanks for answer. I used trjcat again but with following. File Current start (ps) New start (ps) - nvt.trr0.000 ps 0 npt.trr0.000 ps 500 When I get RMSD for final trajectory (1500 ps), I encountered a problem. Figure related to rmsd is unsual in t = 500 ps. https://1drv.ms/u/s!AveJH4Y30cH0sGIhZ1BH99FfMl5W Why? How to resolve it? Looks to me like you re-started the simulation rather than continue it properly from NVT -> NPT, but I have no idea what you did. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] trjcat -settime
Hi Justin, Thanks for answer. I used trjcat again but with following. File Current start (ps) New start (ps) - nvt.trr0.000 ps 0 npt.trr0.000 ps 500 When I get RMSD for final trajectory (1500 ps), I encountered a problem. Figure related to rmsd is unsual in t = 500 ps. https://1drv.ms/u/s!AveJH4Y30cH0sGIhZ1BH99FfMl5W Why? How to resolve it? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs 2018 compilation problem with stdlib
Hi, Currently I have two versions of icc, 18 and 17, but I have already set the environment variables in order to use only icc 17 and icpc 17, that's because cuda-9.1 is not compatible with 18 version of intel's compilers. If I make use of icc 18 I'll get NVCC/C broken warning and the cmake will fail. Sent from TypeApp On Jul 14, 2018, 02:54, at 02:54, David van der Spoel wrote: >Den 2018-07-14 kl. 04:58, skrev Manoel Barrionuevo: >> Hi all, >> >> I'm trying to compile gromacs 2018.2 and I would like to use intel >> compilers along with nvidia gpu graphic (GTX 1060) card in a desktop >> computer with a intel i5 quad-core cpu (the only purpose of it is for > >> learning), in order to do so I was first following the suggested >> procedures at the INSTALL file distributed along with gromacs, and >got >> the command bellow: >> >> cmake ../ -DGMX_FFT_LIBRARY="mkl" -DMKL_LIBRARIES="-Wl,--start-group >> /opt/intel17/mkl/lib/intel64/libmkl_intel_ilp64.a >> /opt/intel17/mkl/lib/intel64/libmkl_gnu_thread.a >> /opt/intel17/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lgomp >> -lpthread -lm -ldl" -DMKL_INCLUDE_DIR="/opt/intel17/mkl/include" >> -DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR="/usr/local/cuda-9.1/" >> -DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILER=icc -DGMX_CXX_FLAGS="-g >-O2 >> -std=c++11" >> >> It worths to say that the OS under current operation is Lubuntu >(16.04) >> and it has both gcc-5.4.1 and g++-5.4.1. Everything goes smoothly >> without problems, however I noticed a std failure after issuing the >> "make" command, it says: >> >> >/home/yokai/Programs/gromacs-2018.2/src/gromacs/utility/fatalerror.cpp(250): > >> error: namespace "std" has no member "_Exit" >> std:: _Exit(returnValue); >Which version of the intel compiler are you using? >icc --version might tell you. > >This function should be present since C++11. >https://en.cppreference.com/w/cpp/utility/program/_Exit > >> ^ >> >> >/home/yokai/Programs/gromacs-2018.2/src/gromacs/utility/fatalerror.cpp(251): > >> warning #1628: function declared with "noreturn" does retu >> rn >> } >> ^ >> >> The same problem can be seen if I start from a very simple "cmake >../" >> and "make". What am I doing wrong? Is there some environment >preparation >> step to be done prior to everything else, and what should it be? >> >> I must say that I'm not an expert on compiling things up and I got >> stuck. Could someone help me out? It would be of great help to know >some >> tips from you guys. >> >> Thank you all. >> >> Kind regards, >> > > >-- >David van der Spoel, Ph.D., Professor of Biology >Head of Department, Cell & Molecular Biology, Uppsala University. >Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >http://www.icm.uu.se >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
On 7/14/18 5:03 AM, farial tavakoli wrote:
Dear justin
I am trying to run a simulation on my complex which has small molecule as a ligand ,
using OPLSAA ff. so I downloaded the topolgen-1.1.tgz and then installed perl script on
linux. then typed "perl -v" to check if it is installed. the perl 5.20.1 was
installed.
but when I typed " perl topolgen.pl -f input.pdb -o output.top [-type itp/top]
" command to generate ligand topology , faced with this error:
Can't open perl script "topolgen.pl": No such file or directory
Infact I am new user in generation topology for small molecules using OPLSAA
ff. Would you please help me to figure out this problem?
"No such file or directory" means the file isn't in the working
directory. This is a generic error message from your shell and nothing
specific about the script itself.
-Justin
Farial
best
On Tuesday, February 20, 2018, 10:24:49 PM GMT+3:30, Justin Lemkul
wrote:
On 2/20/18 12:52 PM, farial tavakoli wrote:
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Dear Justin
Thank you for the reply
You meant , to tweak the emtol doesn't have noticable affects on the
conformational enssemble generated by MD?
Precisely what I said, yes.
-Justin
Sent from Yahoo Mail for iPhone
On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul wrote:
On 2/20/18 4:52 AM, farial tavakoli wrote:
Dear GMX users
I used CHARMM36 all atom force field to generate .top and .gro files for my
complex composed of a receptor protein and a ligand with 2 phosphotyrosine
residues, then ran a md simulation on it and then used g_mmpbsa to calculate
the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol,
respectively. While, I calculated binding energy before for many other
complexes without any phosphate groups using OPLS all atom force field and pdie
= 2 and obtained minus energy. But this time , I dont know why I got positive
binding energy? Is it because of charmm36 all atom force field , the phosphate
groups or it is needed to be energy minimized under more restriction situations?
I am checking different factors to understand its reason, so I wanted to know ,
would it be ok if I energy minimize the complex with more restriction
situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 ?
I think the positive binding energy might be because of the complex didnt
minimized well. however I checked the em.log file and saw it was minimized well:
Steepest Descents converged to Fmax < 1000 in 241 steps
Potential Energy = -6.5047744e+05
Maximum force = 9.8285083e+02 on atom 3335
Norm of force = 3.6905827e+01
Is there anyone can advice me in energy minimization with emtol 800?
The purpose of energy minimization is to establish a reasonable starting
point for your simulation. Tweaks to emtol will have little to no
noticeable bearing on the conformational ensemble generated by MD.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trjcat -settime
On 7/14/18 5:23 AM, Atila Petrosian wrote: Dear gromacs users, I did 2 md simulations: first 500 ps (a.trr) and second 1000 ps (b.trr). I want to join these trajectories. I used following command: gmx trjconv -f a.trr b.trr -o all.trr -settime Summary of files and start times used: File Current start (ps) New start (ps) -- nvt.trr0.000 ps 0 npt.trr0.000 ps 600 Is my manner true? If the second is supposed to start at 500 ps, then you shouldn't be specifying 600 ps, but otherwise, yes, this is the approach to take. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Patch for the Acetylated caps
Hi, Residues for those are present in the type database in some force fields, but there's no ability for GROMACS to build the atoms on for you. Mark On Sat, Jul 14, 2018, 00:22 Shreyas Kaptan wrote: > Dear All, > > I am curious if there exists a patch for the acetylated termini (ACE/CT3) > as provided by the charmm-gui for, gromacs. > > I would be grateful if someone has a systematic solution to adding these > for pdb2gmx. > > Shreyas > > -- > Shreyas Sanjay Kaptan > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] trjcat -settime
Dear gromacs users, I did 2 md simulations: first 500 ps (a.trr) and second 1000 ps (b.trr). I want to join these trajectories. I used following command: gmx trjconv -f a.trr b.trr -o all.trr -settime Summary of files and start times used: File Current start (ps) New start (ps) -- nvt.trr0.000 ps 0 npt.trr0.000 ps 600 Is my manner true? Any help will highly appreciated. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
