[gmx-users] Reviewing docking resluts
Hi everyone This may be irrelevant to the list but i have a big problem. I have designed some inhibitors using molecular docking and then performed 10 nsmd simulations. I have to submit the article for publication. But the journal is asking for the names of persons to review the article. Can you please suggest me some reviewers who are willing to review the article for the journal?. Any suggestions will be highly appreciated Regards -- 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] Average rmsd
ok thanks i'll try this Regards On Mon, Apr 29, 2019 at 5:23 AM Justin Lemkul wrote: > > > On 4/25/19 8:49 AM, neelam wafa wrote: > > Hi! > > I have run 5ns simulation of protein ligand complex and got its rmsd plot > > using gmx_rms. How can i get average rmsd value for this simulation. Is > it > > to be taken from xmgrace graph or there is any way to calculate it? U > cant > > find it in log file. > > You can get the average of any data series (as well as other statistical > analysis) with gmx analyze. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 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. > -- 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] Average rmsd
Ok i ll try Thanks On Mon, 29 Apr 2019, 7:06 am Neena Susan Eappen, < neena.susaneap...@mail.utoronto.ca> wrote: > Hi Neelam, > > I do not have Xmgrace tool, but you can open up the xvg file on excel and > calculate average. > -- > 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] query about different number of solvent molecules added
Thanks sir Mark It means the results are not faulty and I can continue for further work. Thanks for your valuable suggestions. Regards On Sat, 20 Apr 2019, 11:37 pm Mark Abraham, wrote: > Hi, > > Naturally such differences in system preparation are inevitable, and can be > seen before any expensive simulation runs. So the absolute energies are > different for different systems, but fortunately there was little to no > value in comparing them even when they are formally comparable. However > estimates of quantities based on energy differences, such as relative free > energies of binding can be usefully made. > > Mark > > On Sat., 20 Apr. 2019, 14:17 neelam wafa, wrote: > > > Hi! > > Dear Sir Justin. > > I have run 5 ns simulations of two different enzymes in unbound form and > in > > complex with 4 different inhibitors each. Now when I compare the data I > see > > different number of solvent molecules added in each case( solvent being > > water) enzyme 1 has +1 charge and neutrallized with one chloride ion > while > > enzyme 2 has -7 charge and neutralized with 7 sodium ions. the number > > solvent molecules added are followings. > > Enzyme 1enzyme 2 > > free enzyme 21082 20169 > > ligand1 2107320184 > > ligand 2 21070 20151 > > ligand3 20916 20150 > > ligand 4 20901 20150 > > please tell me does it show any fault in the simulation or how can i > > interpret it? similarly there are slight diffrences in the total energy > and > > density of the system while all my ligands have similar structures > > differing only in one or two atoms. > > I have done all my work with your guidance as i have no other expert here > > to guide me and now need little more guidance. can you suggest me some > > literature regarding interpretation of such matters.Thanks in advance. > > Regards > > Neelam Wafa > > Ph. D scholar > > University of the Punjab Lahore, Pakistan > > -- > > 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. > -- 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] query about different number of solvent molecules added
Hi! Dear Sir Justin. I have run 5 ns simulations of two different enzymes in unbound form and in complex with 4 different inhibitors each. Now when I compare the data I see different number of solvent molecules added in each case( solvent being water) enzyme 1 has +1 charge and neutrallized with one chloride ion while enzyme 2 has -7 charge and neutralized with 7 sodium ions. the number solvent molecules added are followings. Enzyme 1enzyme 2 free enzyme 21082 20169 ligand1 2107320184 ligand 2 21070 20151 ligand3 20916 20150 ligand 4 20901 20150 please tell me does it show any fault in the simulation or how can i interpret it? similarly there are slight diffrences in the total energy and density of the system while all my ligands have similar structures differing only in one or two atoms. I have done all my work with your guidance as i have no other expert here to guide me and now need little more guidance. can you suggest me some literature regarding interpretation of such matters.Thanks in advance. Regards Neelam Wafa Ph. D scholar University of the Punjab Lahore, Pakistan -- 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] ACPYPE not working.
Ok thanks. On Sat, 3 Nov 2018, 1:46 pm Alan Ok, I'm still using Amber16, yours is 2018. I believe that they made FATAL > error now the warning we used to have with 2016 version. > > There's nothing I can do. Please, seek Amber mailing list help. > > Alan > > On Fri, 2 Nov 2018 at 19:03, neelam wafa wrote: > > > Hi! > > This is the command I use > > dr@dr-HP-1000-Notebook-PC:~/Downloads/acpype/test$ ../acpype.py -di > > H16.mol2 -c gas > > and the output is: > > | ACPYPE: AnteChamber PYthon Parser interfacE v. 2018-09-20T16:44:17UTC > (c) > > 2018 AWSdS | > > > > > > > DEBUG: Python Version 3.4.3 (default, Nov 28 2017, 16:41:13) > > [GCC 4.8.4] > > DEBUG: Max execution time tolerance is 10h > > WARNING: no 'babel' executable, no PDB file as input can be used! > > DEBUG: /home/dr/Downloads/amber18/bin/antechamber -i H16.mol2 -fi mol2 -o > > tmp -fo ac -pf y > > DEBUG: > > Welcome to antechamber 17.3: molecular input file processor. > > > > acdoctor mode is on: check and diagnosis problems in the input file. > > -- Check Format for mol2 File -- > >Status: pass > > -- Check Unusual Elements -- > >Status: pass > > -- Check Open Valences -- > >Status: pass > > -- Check Geometry -- > > for those bonded > > for those not bonded > >Status: pass > > -- Check Weird Bonds -- > > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error! > > Weird atomic valence (3) for atom (ID: 2, Name: C1). > >Possible open valence. > > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > > File "../acpype.py", line 3704, in > > File "../acpype.py", line 3392, in __init__ > > File "../acpype.py", line 910, in setResNameCheckCoords > > Total time of execution: less than a second > > > > Looking forward for your suggestions > > Regards > > > > On Thu, Nov 1, 2018 at 10:05 PM Alan wrote: > > > > > Please, post here the command you're using (add -d anyway for debug) > and > > > show the whole output. > > > > > > Thanks, > > > > > > Alan > > > > > > On Thu, 1 Nov 2018 at 20:04, neelam wafa > wrote: > > > > > > > Yes it the same one. And the tests are running okay. Problem is with > my > > > > files. > > > > > > > > On Fri, 2 Nov 2018, 12:56 am Alan > > > > > > > > Indeed, it worked, though the warning is important. Are you using > the > > > > > latest ACPYPE? > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > | ACPYPE: AnteChamber PYthon Parser interfacE v. > > 2018-09-20T16:44:17UTC > > > > (c) > > > > > 2018 AWSdS | > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Thu, 1 Nov 2018 at 19:46, neelam wafa > > > wrote: > > > > > > > > > > > Means this file worked well on your system? > > > > > > > > > > > > On Fri, 2 Nov 2018, 12:38 am Alan > > > > > > > > > > > > This kind of problem is due to ANTECHAMBER, not ACPYPE. You may > > try > > > > to > > > > > > get > > > > > > > help at AMBER mailing list. > > > > > > > > > > > > > > For an example I was given, running here: > > > > > > > acpype -di H16.mol2 -c gas > > > > > > > > > > > > > > DEBUG: /Users/alan/Programmes/amber16/bin/*antechamber* -i > > H16.mol2 > > > > -fi > > > > > > > mol2 -o tmp -fo ac -pf y > > > > > > > DEBUG: > > > > > > > Warning: the assigned bond types may be wrong, please : > > > > > > > (1) double check the structure (the connectivity) and/or > > > > > > > (2) adjust atom valence penalty parameters in APS.DAT, and/or > > > > > > > (3) increase PSCUTOFF in define.h and recompile bondtype.c > > > > > > > Be cautious, use a l
Re: [gmx-users] ACPYPE not working.
If I don't use -d then this is the result: | ACPYPE: AnteChamber PYthon Parser interfacE v. 2018-09-20T16:44:17UTC (c) 2018 AWSdS | WARNING: no 'babel' executable, no PDB file as input can be used! ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' Total time of execution: less than a second Regards On Fri, Nov 2, 2018 at 7:02 PM neelam wafa wrote: > Hi! > This is the command I use > dr@dr-HP-1000-Notebook-PC:~/Downloads/acpype/test$ ../acpype.py -di > H16.mol2 -c gas > and the output is: > | ACPYPE: AnteChamber PYthon Parser interfacE v. 2018-09-20T16:44:17UTC > (c) 2018 AWSdS | > > > DEBUG: Python Version 3.4.3 (default, Nov 28 2017, 16:41:13) > [GCC 4.8.4] > DEBUG: Max execution time tolerance is 10h > WARNING: no 'babel' executable, no PDB file as input can be used! > DEBUG: /home/dr/Downloads/amber18/bin/antechamber -i H16.mol2 -fi mol2 -o > tmp -fo ac -pf y > DEBUG: > Welcome to antechamber 17.3: molecular input file processor. > > acdoctor mode is on: check and diagnosis problems in the input file. > -- Check Format for mol2 File -- >Status: pass > -- Check Unusual Elements -- >Status: pass > -- Check Open Valences -- >Status: pass > -- Check Geometry -- > for those bonded > for those not bonded >Status: pass > -- Check Weird Bonds -- > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error! > Weird atomic valence (3) for atom (ID: 2, Name: C1). >Possible open valence. > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > File "../acpype.py", line 3704, in > File "../acpype.py", line 3392, in __init__ > File "../acpype.py", line 910, in setResNameCheckCoords > Total time of execution: less than a second > > Looking forward for your suggestions > Regards > > On Thu, Nov 1, 2018 at 10:05 PM Alan wrote: > >> Please, post here the command you're using (add -d anyway for debug) and >> show the whole output. >> >> Thanks, >> >> Alan >> >> On Thu, 1 Nov 2018 at 20:04, neelam wafa wrote: >> >> > Yes it the same one. And the tests are running okay. Problem is with my >> > files. >> > >> > On Fri, 2 Nov 2018, 12:56 am Alan > > >> > > Indeed, it worked, though the warning is important. Are you using the >> > > latest ACPYPE? >> > > >> > > >> > > >> > >> ==== >> > > | ACPYPE: AnteChamber PYthon Parser interfacE v. >> 2018-09-20T16:44:17UTC >> > (c) >> > > 2018 AWSdS | >> > > >> > > >> > >> >> > > >> > > >> > > On Thu, 1 Nov 2018 at 19:46, neelam wafa >> wrote: >> > > >> > > > Means this file worked well on your system? >> > > > >> > > > On Fri, 2 Nov 2018, 12:38 am Alan > > > > >> > > > > This kind of problem is due to ANTECHAMBER, not ACPYPE. You may >> try >> > to >> > > > get >> > > > > help at AMBER mailing list. >> > > > > >> > > > > For an example I was given, running here: >> > > > > acpype -di H16.mol2 -c gas >> > > > > >> > > > > DEBUG: /Users/alan/Programmes/amber16/bin/*antechamber* -i >> H16.mol2 >> > -fi >> > > > > mol2 -o tmp -fo ac -pf y >> > > > > DEBUG: >> > > > > Warning: the assigned bond types may be wrong, please : >> > > > > (1) double check the structure (the connectivity) and/or >> > > > > (2) adjust atom valence penalty parameters in APS.DAT, and/or >> > > > > (3) increase PSCUTOFF in define.h and recompile bondtype.c >> > > > > Be cautious, use a large value of PSCUTOFF (>100) will >> > > significantly >> > > > > increase the computation time >> > > > > >> > > > > >> > > > > On Thu, 1 Nov 2018 at 08:53, neelam wafa >> > > wrote: >> > > > > >> > > > > > Hi! >> > > > > > Dear all >> > > > > > I am using acpype to generate topologies of ligand for gromacs >> md >>
Re: [gmx-users] ACPYPE not working.
Hi! This is the command I use dr@dr-HP-1000-Notebook-PC:~/Downloads/acpype/test$ ../acpype.py -di H16.mol2 -c gas and the output is: | ACPYPE: AnteChamber PYthon Parser interfacE v. 2018-09-20T16:44:17UTC (c) 2018 AWSdS | DEBUG: Python Version 3.4.3 (default, Nov 28 2017, 16:41:13) [GCC 4.8.4] DEBUG: Max execution time tolerance is 10h WARNING: no 'babel' executable, no PDB file as input can be used! DEBUG: /home/dr/Downloads/amber18/bin/antechamber -i H16.mol2 -fi mol2 -o tmp -fo ac -pf y DEBUG: Welcome to antechamber 17.3: molecular input file processor. acdoctor mode is on: check and diagnosis problems in the input file. -- Check Format for mol2 File -- Status: pass -- Check Unusual Elements -- Status: pass -- Check Open Valences -- Status: pass -- Check Geometry -- for those bonded for those not bonded Status: pass -- Check Weird Bonds -- /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error! Weird atomic valence (3) for atom (ID: 2, Name: C1). Possible open valence. ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' File "../acpype.py", line 3704, in File "../acpype.py", line 3392, in __init__ File "../acpype.py", line 910, in setResNameCheckCoords Total time of execution: less than a second Looking forward for your suggestions Regards On Thu, Nov 1, 2018 at 10:05 PM Alan wrote: > Please, post here the command you're using (add -d anyway for debug) and > show the whole output. > > Thanks, > > Alan > > On Thu, 1 Nov 2018 at 20:04, neelam wafa wrote: > > > Yes it the same one. And the tests are running okay. Problem is with my > > files. > > > > On Fri, 2 Nov 2018, 12:56 am Alan > > > > Indeed, it worked, though the warning is important. Are you using the > > > latest ACPYPE? > > > > > > > > > > > > > > > | ACPYPE: AnteChamber PYthon Parser interfacE v. 2018-09-20T16:44:17UTC > > (c) > > > 2018 AWSdS | > > > > > > > > > > > > > > > > > > On Thu, 1 Nov 2018 at 19:46, neelam wafa > wrote: > > > > > > > Means this file worked well on your system? > > > > > > > > On Fri, 2 Nov 2018, 12:38 am Alan > > > > > > > > This kind of problem is due to ANTECHAMBER, not ACPYPE. You may try > > to > > > > get > > > > > help at AMBER mailing list. > > > > > > > > > > For an example I was given, running here: > > > > > acpype -di H16.mol2 -c gas > > > > > > > > > > DEBUG: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 > > -fi > > > > > mol2 -o tmp -fo ac -pf y > > > > > DEBUG: > > > > > Warning: the assigned bond types may be wrong, please : > > > > > (1) double check the structure (the connectivity) and/or > > > > > (2) adjust atom valence penalty parameters in APS.DAT, and/or > > > > > (3) increase PSCUTOFF in define.h and recompile bondtype.c > > > > > Be cautious, use a large value of PSCUTOFF (>100) will > > > significantly > > > > > increase the computation time > > > > > > > > > > > > > > > On Thu, 1 Nov 2018 at 08:53, neelam wafa > > > wrote: > > > > > > > > > > > Hi! > > > > > > Dear all > > > > > > I am using acpype to generate topologies of ligand for gromacs md > > > > > > simmulation. I habe amber tools 18 and downloaded acpype from > > github. > > > > The > > > > > > test runs go well but when i run my file with ../acpype.py -i > > > UNL.mol2 > > > > > -c > > > > > > gas or even > > > > > > ../acpype.py -di UNL.mol2 > > > > > > iI get following error > > > > > > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: > Fatal > > > > Error! > > > > > > Weird atomic valence (2) for atom (ID: 1, Name: C). > > > > > >Possible open valence. > > > > > > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > > > > > > File "../acpype.py", line 3704, in > > > > > > File "../acpype.py", line 3392, in __init__ > >
Re: [gmx-users] ACPYPE not working.
Yes it the same one. And the tests are running okay. Problem is with my files. On Fri, 2 Nov 2018, 12:56 am Alan Indeed, it worked, though the warning is important. Are you using the > latest ACPYPE? > > > > | ACPYPE: AnteChamber PYthon Parser interfacE v. 2018-09-20T16:44:17UTC (c) > 2018 AWSdS | > > > > > On Thu, 1 Nov 2018 at 19:46, neelam wafa wrote: > > > Means this file worked well on your system? > > > > On Fri, 2 Nov 2018, 12:38 am Alan > > > > This kind of problem is due to ANTECHAMBER, not ACPYPE. You may try to > > get > > > help at AMBER mailing list. > > > > > > For an example I was given, running here: > > > acpype -di H16.mol2 -c gas > > > > > > DEBUG: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 -fi > > > mol2 -o tmp -fo ac -pf y > > > DEBUG: > > > Warning: the assigned bond types may be wrong, please : > > > (1) double check the structure (the connectivity) and/or > > > (2) adjust atom valence penalty parameters in APS.DAT, and/or > > > (3) increase PSCUTOFF in define.h and recompile bondtype.c > > > Be cautious, use a large value of PSCUTOFF (>100) will > significantly > > > increase the computation time > > > > > > > > > On Thu, 1 Nov 2018 at 08:53, neelam wafa > wrote: > > > > > > > Hi! > > > > Dear all > > > > I am using acpype to generate topologies of ligand for gromacs md > > > > simmulation. I habe amber tools 18 and downloaded acpype from github. > > The > > > > test runs go well but when i run my file with ../acpype.py -i > UNL.mol2 > > > -c > > > > gas or even > > > > ../acpype.py -di UNL.mol2 > > > > iI get following error > > > > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal > > Error! > > > > Weird atomic valence (2) for atom (ID: 1, Name: C). > > > >Possible open valence. > > > > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > > > > File "../acpype.py", line 3704, in > > > > File "../acpype.py", line 3392, in __init__ > > > > File "../acpype.py", line 910, in setResNameCheckCoords > > > > Total time of execution: less than a second > > > > Please any way to get out of this problem? Looking forward for your > > > > cooperation > > > > Regards > > > > -- > > > > 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. > > > > > > > > > > > > > -- > > > *I** have just cycled* from Land's End to John O'Groats (the > > > whole Britain!) > > > for a charity, would you consider supporting my cause? > > > http://uk.virginmoneygiving.com/AlanSilva > > > -- > > > Alan Wilter SOUSA da SILVA, DSc > > > Senior Bioinformatician, UniProt > > > European Bioinformatics Institute (EMBL-EBI) > > > European Molecular Biology Laboratory > > > Wellcome Trust Genome Campus > > > Hinxton > > > Cambridge CB10 1SD > > > United Kingdom > > > Tel: +44 (0)1223 494588 > > > -- > > > 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_
Re: [gmx-users] ACPYPE not working.
Means this file worked well on your system? On Fri, 2 Nov 2018, 12:38 am Alan This kind of problem is due to ANTECHAMBER, not ACPYPE. You may try to get > help at AMBER mailing list. > > For an example I was given, running here: > acpype -di H16.mol2 -c gas > > DEBUG: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 -fi > mol2 -o tmp -fo ac -pf y > DEBUG: > Warning: the assigned bond types may be wrong, please : > (1) double check the structure (the connectivity) and/or > (2) adjust atom valence penalty parameters in APS.DAT, and/or > (3) increase PSCUTOFF in define.h and recompile bondtype.c > Be cautious, use a large value of PSCUTOFF (>100) will significantly > increase the computation time > > > On Thu, 1 Nov 2018 at 08:53, neelam wafa wrote: > > > Hi! > > Dear all > > I am using acpype to generate topologies of ligand for gromacs md > > simmulation. I habe amber tools 18 and downloaded acpype from github. The > > test runs go well but when i run my file with ../acpype.py -i UNL.mol2 > -c > > gas or even > > ../acpype.py -di UNL.mol2 > > iI get following error > > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error! > > Weird atomic valence (2) for atom (ID: 1, Name: C). > >Possible open valence. > > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > > File "../acpype.py", line 3704, in > > File "../acpype.py", line 3392, in __init__ > > File "../acpype.py", line 910, in setResNameCheckCoords > > Total time of execution: less than a second > > Please any way to get out of this problem? Looking forward for your > > cooperation > > Regards > > -- > > 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. > > > > > -- > *I** have just cycled* from Land's End to John O'Groats (the > whole Britain!) > for a charity, would you consider supporting my cause? > http://uk.virginmoneygiving.com/AlanSilva > -- > Alan Wilter SOUSA da SILVA, DSc > Senior Bioinformatician, UniProt > European Bioinformatics Institute (EMBL-EBI) > European Molecular Biology Laboratory > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > United Kingdom > Tel: +44 (0)1223 494588 > -- > 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] ACPYPE not working.
Yes i have sourced antechamber and both antechamber -h and acpype -h command work. When i run command acpype.py -i ligand.mol2 It says no such file or directory 'temp' With acpype.py -di ligand.mol2 its gives above error. On Thu, 1 Nov 2018, 4:46 pm Ali Khodayari Have you tried to source amber before commanding acpype for the conversion? > Apparently it’s looking for antechamber but it can’t access it. > When amber is sourced first, you can get a result from commands such as > antechamber -h > Try to first source your amber, and then run acpype. > > > On 1 Nov 2018, at 09:52, neelam wafa wrote: > > > > Hi! > > Dear all > > I am using acpype to generate topologies of ligand for gromacs md > > simmulation. I habe amber tools 18 and downloaded acpype from github. The > > test runs go well but when i run my file with ../acpype.py -i UNL.mol2 > -c > > gas or even > > ../acpype.py -di UNL.mol2 > > iI get following error > > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error! > > Weird atomic valence (2) for atom (ID: 1, Name: C). > > Possible open valence. > > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > > File "../acpype.py", line 3704, in > > File "../acpype.py", line 3392, in __init__ > > File "../acpype.py", line 910, in setResNameCheckCoords > > Total time of execution: less than a second > > Please any way to get out of this problem? Looking forward for your > > cooperation > > Regards > > -- > > 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. -- 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] ACPYPE not working.
Hi! Dear all I am using acpype to generate topologies of ligand for gromacs md simmulation. I habe amber tools 18 and downloaded acpype from github. The test runs go well but when i run my file with ../acpype.py -i UNL.mol2 -c gas or even ../acpype.py -di UNL.mol2 iI get following error /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error! Weird atomic valence (2) for atom (ID: 1, Name: C). Possible open valence. ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' File "../acpype.py", line 3704, in File "../acpype.py", line 3392, in __init__ File "../acpype.py", line 910, in setResNameCheckCoords Total time of execution: less than a second Please any way to get out of this problem? Looking forward for your cooperation Regards -- 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] Acpype failed Errno2
Hi I am using acpype . I have amber tools 18. I get an error. When I run my ligand file for topology i got ACPYPE failed: Errno 2 no such file or directory: 'temp'. Any suggestion for the problem . Thanks in advance. Regards Show quoted text -- 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] acpype
I have by defalt python 2.7.6 and python 3.4.3 Regards On Tue, 30 Oct 2018, 1:11 am Alan, wrote: > Are you running python3? > > what > > python -V > > or > > python3 -V > > outputs? > > Alan > > On Mon, 29 Oct 2018 at 13:25, neelam wafa wrote: > > > Hi > > Thanks for your help. I have resolved that problem but got another one . > > when I run the command > > > > ../acpype.py -i FFF.pdb > > > > I get this error. > > File "../acpype.py", line 561 > > def __init__(self) -> None: > >^ > > SyntaxError: invalid syntax > > > > can you please help me out of the situation? > > > > Thanks in advance > > > > Regards > > > > > > > > On Thu, Oct 25, 2018 at 4:02 PM Alan wrote: > > > > > Check your python3, what's the command line for your python3? > > > > > > The shebang line (first line) in acpype.py is: > > > > > > #!/usr/bin/env python3 > > > > > > you need python3 to run acpype. If your default python is already > > python3, > > > then change line to > > > > > > #!/usr/bin/env python > > > > > > python -V > > > > > > tells which python version you have. > > > > > > Thanks, > > > > > > Alan > > > > > > On Thu, 25 Oct 2018 at 16:44, neelam wafa > wrote: > > > > > > > Hi, Alan > > > > > > > > I have installed amber tools 18 for antechamber and acpype with > > > > > > > > git clone https://github.com/alanwilter/acpype.git > > > > > > > > then installed it with > > > > ln -s $PWD/acpype.py /usr/local/bin/acpype > > > > > > > > I didn't install open babel because my input files are in mol2 > format. > > > > when i reun the command acpype -h or acpype i ligand.mol2 > > > > > > > > it says, acpype command not found. > > > > > > > > please help me about how to use acpype to generate ligand topology as > > > > i have been the online acpype server for the purpose. > > > > > > > > thanks in advance. > > > > > > > > Regards > > > > > > > > > > > > On Wed, Oct 24, 2018 at 9:29 PM Alan wrote: > > > > > > > > > We are working on it now. I can't tell you exactly because we need > > > > several > > > > > tests. It's a complete new version re-written from scratch. > > > > > > > > > > I'm really sorry for the inconvenience but we hope to bring it back > > in > > > a > > > > > month or two. > > > > > > > > > > Alan > > > > > > > > > > On Wed, 24 Oct 2018 at 16:58, neelam wafa > > > wrote: > > > > > > > > > > > Hi alan > > > > > > > > > > > > Can you please tell how long will it take for the online acpype > > > server > > > > to > > > > > > be available? > > > > > > > > > > > > Regards > > > > > > Neelam wafa > > > > > > > > > > > > On Wed, 24 Oct 2018, 6:23 pm Alan, wrote: > > > > > > > > > > > > > Indeed, it's mostly Luciano spearheading these new things. > > > Hopefully, > > > > > we > > > > > > > will have more things to show eventually. > > > > > > > > > > > > > > Alan > > > > > > > > > > > > > > On Wed, 24 Oct 2018 at 14:14, Bhupendra Dandekar < > > > > > > > bhupendra.dandekar...@gmail.com> wrote: > > > > > > > > > > > > > > > I actually got lot of help from Luciano Kagami about > > installation > > > > and > > > > > > > usage > > > > > > > > of acpype and ligro. > > > > > > > > Thanks to both of you. > > > > > > > > > > > > > > > > Bhupendra > > > > > > > > > > > > > > > > On Wed, Oct 24, 2018 at 6:38 PM Bhupendra Dandekar < > > > > > > > > bhupendra.dandekar...@gmail.com> wrote: > > > > > > > > > > > > > > > > > Thanks to you also sir. > > > > >
Re: [gmx-users] acpype
Hi Thanks for your help. I have resolved that problem but got another one . when I run the command ../acpype.py -i FFF.pdb I get this error. File "../acpype.py", line 561 def __init__(self) -> None: ^ SyntaxError: invalid syntax can you please help me out of the situation? Thanks in advance Regards On Thu, Oct 25, 2018 at 4:02 PM Alan wrote: > Check your python3, what's the command line for your python3? > > The shebang line (first line) in acpype.py is: > > #!/usr/bin/env python3 > > you need python3 to run acpype. If your default python is already python3, > then change line to > > #!/usr/bin/env python > > python -V > > tells which python version you have. > > Thanks, > > Alan > > On Thu, 25 Oct 2018 at 16:44, neelam wafa wrote: > > > Hi, Alan > > > > I have installed amber tools 18 for antechamber and acpype with > > > > git clone https://github.com/alanwilter/acpype.git > > > > then installed it with > > ln -s $PWD/acpype.py /usr/local/bin/acpype > > > > I didn't install open babel because my input files are in mol2 format. > > when i reun the command acpype -h or acpype i ligand.mol2 > > > > it says, acpype command not found. > > > > please help me about how to use acpype to generate ligand topology as > > i have been the online acpype server for the purpose. > > > > thanks in advance. > > > > Regards > > > > > > On Wed, Oct 24, 2018 at 9:29 PM Alan wrote: > > > > > We are working on it now. I can't tell you exactly because we need > > several > > > tests. It's a complete new version re-written from scratch. > > > > > > I'm really sorry for the inconvenience but we hope to bring it back in > a > > > month or two. > > > > > > Alan > > > > > > On Wed, 24 Oct 2018 at 16:58, neelam wafa > wrote: > > > > > > > Hi alan > > > > > > > > Can you please tell how long will it take for the online acpype > server > > to > > > > be available? > > > > > > > > Regards > > > > Neelam wafa > > > > > > > > On Wed, 24 Oct 2018, 6:23 pm Alan, wrote: > > > > > > > > > Indeed, it's mostly Luciano spearheading these new things. > Hopefully, > > > we > > > > > will have more things to show eventually. > > > > > > > > > > Alan > > > > > > > > > > On Wed, 24 Oct 2018 at 14:14, Bhupendra Dandekar < > > > > > bhupendra.dandekar...@gmail.com> wrote: > > > > > > > > > > > I actually got lot of help from Luciano Kagami about installation > > and > > > > > usage > > > > > > of acpype and ligro. > > > > > > Thanks to both of you. > > > > > > > > > > > > Bhupendra > > > > > > > > > > > > On Wed, Oct 24, 2018 at 6:38 PM Bhupendra Dandekar < > > > > > > bhupendra.dandekar...@gmail.com> wrote: > > > > > > > > > > > > > Thanks to you also sir. > > > > > > > Your work is really appreciated and is really helpful. > > > > > > > > > > > > > > > > > > > > > Bhupendra > > > > > > > > > > > > > > On Wed, Oct 24, 2018 at 3:59 PM Alan > > wrote: > > > > > > > > > > > > > >> Thanks Bhupendra, indeed we have this option, which is > > > experimental, > > > > > but > > > > > > >> I'm glad to see some are already using it and it seems to be > > > > working. > > > > > > >> > > > > > > >> Alan > > > > > > >> > > > > > > >> On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar < > > > > > > >> bhupendra.dandekar...@gmail.com> wrote: > > > > > > >> > > > > > > >> > Dear Farial, > > > > > > >> > > > > > > > >> > Use this command to install acpype and antechamber using > > conda: > > > > > > >> > > > > > > > >> > conda install -c acpype -c openbabel -c ambermd > > > > > > >> > > > > > > > >> > and then you can check and call acpype, antechamber like > th
Re: [gmx-users] acpype
Hi, Alan I have installed amber tools 18 for antechamber and acpype with git clone https://github.com/alanwilter/acpype.git then installed it with ln -s $PWD/acpype.py /usr/local/bin/acpype I didn't install open babel because my input files are in mol2 format. when i reun the command acpype -h or acpype i ligand.mol2 it says, acpype command not found. please help me about how to use acpype to generate ligand topology as i have been the online acpype server for the purpose. thanks in advance. Regards On Wed, Oct 24, 2018 at 9:29 PM Alan wrote: > We are working on it now. I can't tell you exactly because we need several > tests. It's a complete new version re-written from scratch. > > I'm really sorry for the inconvenience but we hope to bring it back in a > month or two. > > Alan > > On Wed, 24 Oct 2018 at 16:58, neelam wafa wrote: > > > Hi alan > > > > Can you please tell how long will it take for the online acpype server to > > be available? > > > > Regards > > Neelam wafa > > > > On Wed, 24 Oct 2018, 6:23 pm Alan, wrote: > > > > > Indeed, it's mostly Luciano spearheading these new things. Hopefully, > we > > > will have more things to show eventually. > > > > > > Alan > > > > > > On Wed, 24 Oct 2018 at 14:14, Bhupendra Dandekar < > > > bhupendra.dandekar...@gmail.com> wrote: > > > > > > > I actually got lot of help from Luciano Kagami about installation and > > > usage > > > > of acpype and ligro. > > > > Thanks to both of you. > > > > > > > > Bhupendra > > > > > > > > On Wed, Oct 24, 2018 at 6:38 PM Bhupendra Dandekar < > > > > bhupendra.dandekar...@gmail.com> wrote: > > > > > > > > > Thanks to you also sir. > > > > > Your work is really appreciated and is really helpful. > > > > > > > > > > > > > > > Bhupendra > > > > > > > > > > On Wed, Oct 24, 2018 at 3:59 PM Alan wrote: > > > > > > > > > >> Thanks Bhupendra, indeed we have this option, which is > experimental, > > > but > > > > >> I'm glad to see some are already using it and it seems to be > > working. > > > > >> > > > > >> Alan > > > > >> > > > > >> On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar < > > > > >> bhupendra.dandekar...@gmail.com> wrote: > > > > >> > > > > >> > Dear Farial, > > > > >> > > > > > >> > Use this command to install acpype and antechamber using conda: > > > > >> > > > > > >> > conda install -c acpype -c openbabel -c ambermd > > > > >> > > > > > >> > and then you can check and call acpype, antechamber like this > from > > > > your > > > > >> > terminal: > > > > >> > > > > > >> > acpype -h > > > > >> > antechamber -h > > > > >> > > > > > >> > then you can generate ligand topology using this command: > > > > >> > > > > > >> > acpype -i FFF.pdb -b FFF -o gmx > > > > >> > > > > > >> > Hope this helps. Let me know if you have any questions. > > > > >> > > > > > >> > Thanks > > > > >> > Bhupendra > > > > >> > > > > > >> > On Wed, Oct 24, 2018 at 2:01 PM Farial Tavakoli < > > > > >> faryal.tavak...@gmail.com > > > > >> > > > > > > >> > wrote: > > > > >> > > > > > >> > > Dear GMX useres > > > > >> > > > > > > >> > > I am trying to convert .OFF and .FRCMOD files obtained from > > AMBER > > > > >> > parameter > > > > >> > > database (Bryce Group: Computational Biophysics and Drug > Design > > - > > > > >> > > University of Manchester) > > > > >> > > <http://sites.pharmacy.manchester.ac.uk/bryce/amber> to the > > > format > > > > >> that > > > > >> > > GROMACS is compatible with in .rtp files*. so referred to > > GROMACS > > > > >> > tutorial > > > > >> > > protein-ligand complex and downloaded acpype
Re: [gmx-users] acpype
Hi alan Can you please tell how long will it take for the online acpype server to be available? Regards Neelam wafa On Wed, 24 Oct 2018, 6:23 pm Alan, wrote: > Indeed, it's mostly Luciano spearheading these new things. Hopefully, we > will have more things to show eventually. > > Alan > > On Wed, 24 Oct 2018 at 14:14, Bhupendra Dandekar < > bhupendra.dandekar...@gmail.com> wrote: > > > I actually got lot of help from Luciano Kagami about installation and > usage > > of acpype and ligro. > > Thanks to both of you. > > > > Bhupendra > > > > On Wed, Oct 24, 2018 at 6:38 PM Bhupendra Dandekar < > > bhupendra.dandekar...@gmail.com> wrote: > > > > > Thanks to you also sir. > > > Your work is really appreciated and is really helpful. > > > > > > > > > Bhupendra > > > > > > On Wed, Oct 24, 2018 at 3:59 PM Alan wrote: > > > > > >> Thanks Bhupendra, indeed we have this option, which is experimental, > but > > >> I'm glad to see some are already using it and it seems to be working. > > >> > > >> Alan > > >> > > >> On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar < > > >> bhupendra.dandekar...@gmail.com> wrote: > > >> > > >> > Dear Farial, > > >> > > > >> > Use this command to install acpype and antechamber using conda: > > >> > > > >> > conda install -c acpype -c openbabel -c ambermd > > >> > > > >> > and then you can check and call acpype, antechamber like this from > > your > > >> > terminal: > > >> > > > >> > acpype -h > > >> > antechamber -h > > >> > > > >> > then you can generate ligand topology using this command: > > >> > > > >> > acpype -i FFF.pdb -b FFF -o gmx > > >> > > > >> > Hope this helps. Let me know if you have any questions. > > >> > > > >> > Thanks > > >> > Bhupendra > > >> > > > >> > On Wed, Oct 24, 2018 at 2:01 PM Farial Tavakoli < > > >> faryal.tavak...@gmail.com > > >> > > > > >> > wrote: > > >> > > > >> > > Dear GMX useres > > >> > > > > >> > > I am trying to convert .OFF and .FRCMOD files obtained from AMBER > > >> > parameter > > >> > > database (Bryce Group: Computational Biophysics and Drug Design - > > >> > > University of Manchester) > > >> > > <http://sites.pharmacy.manchester.ac.uk/bryce/amber> to the > format > > >> that > > >> > > GROMACS is compatible with in .rtp files*. so referred to GROMACS > > >> > tutorial > > >> > > protein-ligand complex and downloaded acpype. installed it using > its > > >> > > readme.txt file but whenever i typed../acpype.py -i FFF.pdb > At > > >> > folder > > >> > > *acpype/test* (/Downloads/acpype-master/acpype) or > > >> > > (/Downloads/acpype-master/acpype/test) faced to this error:* > > >> > > > > >> > > > > >> > > *bash: ../acpype.py: No such file or directory* > > >> > > > > >> > > *while when I typed whereis acpype in terminal , the operating > > system > > >> > says > > >> > > :* > > >> > > > > >> > > > > >> > > *acpype: /usr/local/bin/acpype* > > >> > > * it means there is the executable file of acpype . so how come I > > type > > >> > > ../acpype.py -h or ../acpype -i FFF.pdb , the system says NO such > > >> file or > > >> > > directory?* > > >> > > *Is there anyone who ca help me?* > > >> > > *I really would be appreciated it if one help me to solve this and > > can > > >> > > convert the AMBER format files to GRMACS format files.* > > >> > > > > >> > > *best regards* > > >> > > *Farial* > > >> > > -- > > >> > > Gromacs Users mailing list > > >> > > > > >> > > * Please search the archive at > > >> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > before > > >> > > posting! > > >> > > > > >
Re: [gmx-users] i have queston about partial charge zinc
Hi ! Alan the link for updated acpype you have shared is all about the downloadable tool. Can you please share the link for online server for it. and is their any tutorial to explain the changed protocol. looking forward for your cooperation. Regards On 9/20/18, Alan wrote: > Please, official, original, updated ACPYPE is now here: > https://github.com/alanwilter/acpype > > Alan > > On 20 September 2018 at 13:56, Andrea Coletta > wrote: > >> In general I would say that +2 is not a good choice, since it seems to me >> that this is a Zinc complex. >> >> You may want to look at this: >> >> http://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm >> >> you should be able to create the topology in ambertools and then convert >> it to gromac with acpype (https://github.com/llazzaro/acpype) >> >> -Original Message- >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of milad >> bagheri >> Sent: 20. september 2018 14:28 >> To: gromacs.org_gmx-users@maillist.sys.kth.se >> Subject: [gmx-users] i have queston about partial charge zinc >> >> Hi >> I gonna MD simulation a protein that contained a zinc ion for build >> topology I used from the amber99sb force field Atomic charge is written >> "+2" in topology. >> I wanted to ask if this charge is correct or should be calculated in a >> different way? >> "PDB id 4row" >> sincerely >> -- >> 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. >> > > > > -- > I'll cycle across Britain in 2018 for a charity, would you consider > supporting my cause? http://uk.virginmoneygiving.com/AlanSilva > Many thanks! > -- > Alan Wilter SOUSA da SILVA, DSc > Senior Bioinformatician, UniProt > European Bioinformatics Institute (EMBL-EBI) > European Molecular Biology Laboratory > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > United Kingdom > Tel: +44 (0)1223 494588 > -- > 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] Values of coul_lambda for free energy calculation.
Sir Justin and sir Mark Please comment on my question. I ll be really thankful to you. On Tue, 28 Aug 2018, 11:07 pm neelam wafa, wrote: > Hi gmx users, > I want to calculate free energy of binding for protein ligand complex. In > first step of free energy of solvation when i have to create lambda states > vwd_lambda changes from 0.00 and increases gradually to 1. Can the > coul_lambda be changed fradually after the vwd_lambda becomes 1. > > Kindly need your suggestions. > Regards > -- 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] Values of coul_lambda for free energy calculation.
Hi gmx users, I want to calculate free energy of binding for protein ligand complex. In first step of free energy of solvation when i have to create lambda states vwd_lambda changes from 0.00 and increases gradually to 1. Can the coul_lambda be changed fradually after the vwd_lambda becomes 1. Kindly need your suggestions. Regards -- 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] Fwd: free energy calculation.
Hi everyone. Kindlt need your help urgently. -- Forwarded message - From: neelam wafa Date: Mon, 27 Aug 2018, 3:41 pm Subject: free energy calculation. To: , Hi! Dear gmx users, I have md simmulations of a protein with four different ligands. now I want to calculate the free energy of binding. which method does suit after md simmulation? either g_mmpbsa or gmx BAR method. If I use BAR method is it necessary to set charges to zero as in the tutorial given at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html. I s necessary to turn off couloumb interactions for calculating free energy of ligand protein complex. if i want to use coloumb interactions also then should i set the coul_lambdas values in the same way as vdw_lambdas. Another question is that there is another tutorial available at http://www.gromacs.org/@api/deki/files/262/=gromacs-free-energy-tutorial.pdf In this tutorial the system has been equilliberated before generating the lambda states. while in the justin tutorial each lambda state is equiliberated separately. kindly tell me which one is more suitable for a protein ligand complex. looking forward for your cooperation. sorry if the questions are trivial. Regards Neelam Ph.D scholar -- 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] free energy calculation.
Hi! Dear gmx users, I have md simmulations of a protein with four different ligands. now I want to calculate the free energy of binding. which method does suit after md simmulation? either g_mmpbsa or gmx BAR method. If I use BAR method is it necessary to set charges to zero as in the tutorial given at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html. I s necessary to turn off couloumb interactions for calculating free energy of ligand protein complex. if i want to use coloumb interactions also then should i set the coul_lambdas values in the same way as vdw_lambdas. Another question is that there is another tutorial available at http://www.gromacs.org/@api/deki/files/262/=gromacs-free-energy-tutorial.pdf In this tutorial the system has been equilliberated before generating the lambda states. while in the justin tutorial each lambda state is equiliberated separately. kindly tell me which one is more suitable for a protein ligand complex. looking forward for your cooperation. sorry if the questions are trivial. Regards Neelam Ph.D scholar -- 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] Fwd: problem in energy minimization
Thanks sir Mark, I have compared the complex before and after the minimization. there are slight differences in the bond angles and interactions. overall posture is not much different. Previously I had run a simulation with same problem but the rmsd output was stable. Are these results reliable? Looking forward for your valuable suggestions. Regards On Wed, Jul 18, 2018 at 5:42 PM, neelam wafa wrote: > Thanks sir Mark, > > I have compared the complex before and after the minimization. there are > slight differences in the bond angles and interactions. overall posture is > not much different. I have attached a picture of the pymol session > comparing the two . blue one is after minimization. please have a look on > it. > Previously I had run a simulation with same problem but the rmsd output > was stable. > > Looking forward for your valuable suggestions. > > Regards > > Neelam > > On Wed, Jul 18, 2018 at 9:47 AM, Mark Abraham > wrote: > >> Hi, >> >> That could be fine, as your potential energy is large and negative. We >> can't tell from the outside. Do visualise the before and after to get some >> clues. >> >> Mark >> >> On Tue, Jul 17, 2018, 19:11 neelam wafa wrote: >> >> > -- Forwarded message -- >> > From: neelam wafa >> > Date: Tue, Jul 17, 2018 at 1:12 PM >> > Subject: problem in energy minimization >> > To: gromacs.org_gmx-users@maillist.sys.kth.se >> > >> > >> > Hi, >> > >> > Dear gromacs users, I am running md simmulation of a protein with a >> ligand. >> > i have already done it with the same protein and a different ligand. Now >> > when i run em md run i get following result. >> > >> > Energy minimization has stopped, but the forces have not converged to >> the >> > requested precision Fmax < 1000 (which may not be possible for your >> > system). >> > It stopped because the algorithm tried to make a new step whose size was >> > too >> > small, or there was no change in the energy since last step. Either >> way, we >> > regard the minimization as converged to within the available machine >> > precision, given your starting configuration and EM parameters. >> > >> > Double precision normally gives you higher accuracy, but this is often >> not >> > needed for preparing to run molecular dynamics. >> > You might need to increase your constraint accuracy, or turn >> > off constraints altogether (set constraints = none in mdp file) >> > >> > writing lowest energy coordinates. >> > >> > Steepest Descents converged to machine precision in 150 steps, >> > but did not reach the requested Fmax < 1000. >> > Potential Energy = -9.3659806e+05 >> > Maximum force = 1.0269271e+04 on atom 4399 >> > Norm of force = 9.8929054e+01 >> > >> > NOTE: 10 % of the run time was spent in pair search, >> > you might want to increase nstlist (this has no effect on >> accuracy) >> > please guide me is it reliable to proceede for simmulation. or there is >> > something wrong. Is it a sign of system instability? >> > >> > looking forward for your cooperation. >> > >> > Regards >> > -- >> > 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. >> > > -- 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] Fwd: problem in energy minimization
-- Forwarded message -- From: neelam wafa Date: Tue, Jul 17, 2018 at 1:12 PM Subject: problem in energy minimization To: gromacs.org_gmx-users@maillist.sys.kth.se Hi, Dear gromacs users, I am running md simmulation of a protein with a ligand. i have already done it with the same protein and a different ligand. Now when i run em md run i get following result. Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 150 steps, but did not reach the requested Fmax < 1000. Potential Energy = -9.3659806e+05 Maximum force = 1.0269271e+04 on atom 4399 Norm of force = 9.8929054e+01 NOTE: 10 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) please guide me is it reliable to proceede for simmulation. or there is something wrong. Is it a sign of system instability? looking forward for your cooperation. Regards -- 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] problem in energy minimization
Hi, Dear gromacs users, I am running md simmulation of a protein with a ligand. i have already done it with the same protein and a different ligand. Now when i run em md run i get following result. Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 150 steps, but did not reach the requested Fmax < 1000. Potential Energy = -9.3659806e+05 Maximum force = 1.0269271e+04 on atom 4399 Norm of force = 9.8929054e+01 NOTE: 10 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) please guide me is it reliable to proceede for simmulation. or there is something wrong. Is it a sign of system instability? looking forward for your cooperation. Regards -- 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] increasing md run speed
Dear gmx users! I am running md simmulation of a protein with different ligands but the speed is decreasing with every simmulation. In first one it was 25hrs/ns, for second one it became 35 hrs/ns then 36hs/ns. what can be the reason? I am using this command for the run. How to select the value of x if I use this command to increase the speed. Following is the detail of the cores used and the hardware i am using. Running on 1 node with total 2 cores, 4 logical cores Hardware detected: CPU info: Vendor: GenuineIntel Brand: Intel(R) Core(TM) i3-2370M CPU @ 2.40GHz SIMD instructions most likely to fit this hardware: AVX_256 SIMD instructions selected at GROMACS compile time: AVX_256 Reading file em.tpr, VERSION 5.1.5 (single precision) Using 1 MPI thread Using 4 OpenMP threads Looking forward for your help and cooperation. Regards -- 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] Restarting crashed simmulation.
Thanks sir Justin and sir Mark On Sat, 12 May 2018 3:27 pm Mark Abraham, <mark.j.abra...@gmail.com> wrote: > Hi, > > Or use the existing tool one has for a group of related files, called a > directory or folder ;-) It's not compulsory to do your whole thesis in the > same folder, too :-D > > Mark > > On Fri, May 11, 2018, 21:01 Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 5/11/18 2:11 PM, neelam wafa wrote: > > > Hi! > > > does this means that i should not have used -deffnm md_0_1 in the run > > > command? Actually I am a student and new to gromacs and have no > experties > > > in it. I think I need to read more about md run command options. > > > > Use -deffnm, it saves you typing and makes your life easier, because > > instead of relying on generic, default file names, you know exactly what > > you did and what your files hold. > > > > -Justin > > > > > Regards > > > > > > On Fri, 11 May 2018 10:57 pm Mark Abraham, <mark.j.abra...@gmail.com> > > wrote: > > > > > >> Hi, > > >> > > >> Behaviour has changed since 5.1 to make it harder for this happen, but > > if > > >> you do not call mdrun exactly the same way, older implementations of > > >> checkpointing would try to be helpful and sometimes actually not be > > >> helpful. This only happens if you try to over manage mdrun. It's best > to > > >> leave it alone to append with default file names, or use -noappend > with > > >> default filenames and get the part number added automatically. But if > > you > > >> want to change the filenames to have a part number you manage > yourself, > > you > > >> have to manage everything else too... > > >> > > >> Mark > > >> > > >> On Fri, May 11, 2018 at 7:28 PM neelam wafa <neelam.w...@gmail.com> > > wrote: > > >> > > >>> okay, > > >>> > > >>> Thanks > > >>> > > >>> On Fri, May 11, 2018 at 5:19 PM, Justin Lemkul <jalem...@vt.edu> > > wrote: > > >>> > > >>>> > > >>>> On 5/11/18 1:18 PM, neelam wafa wrote: > > >>>> > > >>>>> *This is the message of gmx check for both the trajectories. I*t > > means > > >>>>> that > > >>>>> trajectory is not continuous. Am I right? > > >>>>> > > >>>> They are continuous (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc > > >>> starts > > >>>> at the same time) and can be concatenated together. It appears your > > run > > >>> did > > >>>> continue from the checkpoint file. I have no explanation for why the > > >> file > > >>>> names are not what one would expect. > > >>>> > > >>>> -Justin > > >>>> > > >>>> *gmx check -f md_0_1.xtc* > > >>>>> Checking file md_0_1.xtc > > >>>>> Reading frame 0 time0.000 > > >>>>> # Atoms 67864 > > >>>>> Precision 0.001 (nm) > > >>>>> Reading frame 200 time 2000.000 > > >>>>> > > >>>>> > > >>>>> Item#frames Timestep (ps) > > >>>>> Step 27310 > > >>>>> Time 27310 > > >>>>> Lambda 0 > > >>>>> Coords 27310 > > >>>>> Velocities 0 > > >>>>> Forces 0 > > >>>>> Box27310 > > >>>>> > > >>>>> * gmx check -f traj_comp.xtc* > > >>>>> > > >>>>> > > >>>>> Checking file traj_comp.xtc > > >>>>> Reading frame 0 time 2720.000 > > >>>>> # Atoms 67864 > > >>>>> Precision 0.001 (nm) > > >>>>> Last frame 13 time 2850.000 > > >>>>> > > >>>>> > > >>>>> Item#frames Timestep (ps) > > >>>>> Step1410 > > >>>>> Time1410 > > >>>>> Lambda 0 > > >>>>> Coords 1410 > > >>>>> Velocities 0 > > >>
Re: [gmx-users] Restarting crashed simmulation.
Hi! does this means that i should not have used -deffnm md_0_1 in the run command? Actually I am a student and new to gromacs and have no experties in it. I think I need to read more about md run command options. Regards On Fri, 11 May 2018 10:57 pm Mark Abraham, <mark.j.abra...@gmail.com> wrote: > Hi, > > Behaviour has changed since 5.1 to make it harder for this happen, but if > you do not call mdrun exactly the same way, older implementations of > checkpointing would try to be helpful and sometimes actually not be > helpful. This only happens if you try to over manage mdrun. It's best to > leave it alone to append with default file names, or use -noappend with > default filenames and get the part number added automatically. But if you > want to change the filenames to have a part number you manage yourself, you > have to manage everything else too... > > Mark > > On Fri, May 11, 2018 at 7:28 PM neelam wafa <neelam.w...@gmail.com> wrote: > > > okay, > > > > Thanks > > > > On Fri, May 11, 2018 at 5:19 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > > > > > On 5/11/18 1:18 PM, neelam wafa wrote: > > > > > >> *This is the message of gmx check for both the trajectories. I*t means > > >> that > > >> trajectory is not continuous. Am I right? > > >> > > > > > > They are continuous (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc > > starts > > > at the same time) and can be concatenated together. It appears your run > > did > > > continue from the checkpoint file. I have no explanation for why the > file > > > names are not what one would expect. > > > > > > -Justin > > > > > > *gmx check -f md_0_1.xtc* > > >> > > >> Checking file md_0_1.xtc > > >> Reading frame 0 time0.000 > > >> # Atoms 67864 > > >> Precision 0.001 (nm) > > >> Reading frame 200 time 2000.000 > > >> > > >> > > >> Item#frames Timestep (ps) > > >> Step 27310 > > >> Time 27310 > > >> Lambda 0 > > >> Coords 27310 > > >> Velocities 0 > > >> Forces 0 > > >> Box27310 > > >> > > >> * gmx check -f traj_comp.xtc* > > >> > > >> > > >> Checking file traj_comp.xtc > > >> Reading frame 0 time 2720.000 > > >> # Atoms 67864 > > >> Precision 0.001 (nm) > > >> Last frame 13 time 2850.000 > > >> > > >> > > >> Item#frames Timestep (ps) > > >> Step1410 > > >> Time1410 > > >> Lambda 0 > > >> Coords 1410 > > >> Velocities 0 > > >> Forces 0 > > >> Box 1410 > > >> > > >> > > >> On Fri, May 11, 2018 at 5:12 PM, neelam wafa <neelam.w...@gmail.com> > > >> wrote: > > >> > > >> The previous command was : > > >>> > > >>> gmx mdrun -deffnm md_0_1 > > >>> > > >>> I didn't ust -cpi falg . > > >>> > > >>> On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul <jalem...@vt.edu> > > wrote: > > >>> > > >>> > > >>>> On 5/11/18 12:52 PM, neelam wafa wrote: > > >>>> > > >>>> I used this command: > > >>>>> gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt > > >>>>> > > >>>>> But I think its not appending as new files are being generated with > > >>>>> names > > >>>>> state.cpt, state_prev.cpt and traj_comp.xtc > > >>>>> while the previous files were md_0_1.cpt, md_0_1_prev.cpt and > > >>>>> md_0_1.xtc. > > >>>>> Why has it happened ? I have checked log files but not able to > infer > > a > > >>>>> proper answer. > > >>>>> > > >>>>> The file names are contained within the .cpt file, and those are > what > > >>>> will be written. You haven't said what your previous command was, > but > > >>>> the > > >>>> use of -deffnm makes this much easier: > > >>>> > > >>>> gmx mdrun -deffnm md_0_1 -cpi > > &
Re: [gmx-users] Restarting crashed simmulation.
okay, Thanks On Fri, May 11, 2018 at 5:19 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/11/18 1:18 PM, neelam wafa wrote: > >> *This is the message of gmx check for both the trajectories. I*t means >> that >> trajectory is not continuous. Am I right? >> > > They are continuous (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc starts > at the same time) and can be concatenated together. It appears your run did > continue from the checkpoint file. I have no explanation for why the file > names are not what one would expect. > > -Justin > > *gmx check -f md_0_1.xtc* >> >> Checking file md_0_1.xtc >> Reading frame 0 time0.000 >> # Atoms 67864 >> Precision 0.001 (nm) >> Reading frame 200 time 2000.000 >> >> >> Item#frames Timestep (ps) >> Step 27310 >> Time 27310 >> Lambda 0 >> Coords 27310 >> Velocities 0 >> Forces 0 >> Box27310 >> >> * gmx check -f traj_comp.xtc* >> >> >> Checking file traj_comp.xtc >> Reading frame 0 time 2720.000 >> # Atoms 67864 >> Precision 0.001 (nm) >> Last frame 13 time 2850.000 >> >> >> Item#frames Timestep (ps) >> Step1410 >> Time1410 >> Lambda 0 >> Coords 1410 >> Velocities 0 >> Forces 0 >> Box 1410 >> >> >> On Fri, May 11, 2018 at 5:12 PM, neelam wafa <neelam.w...@gmail.com> >> wrote: >> >> The previous command was : >>> >>> gmx mdrun -deffnm md_0_1 >>> >>> I didn't ust -cpi falg . >>> >>> On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> On 5/11/18 12:52 PM, neelam wafa wrote: >>>> >>>> I used this command: >>>>> gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt >>>>> >>>>> But I think its not appending as new files are being generated with >>>>> names >>>>> state.cpt, state_prev.cpt and traj_comp.xtc >>>>> while the previous files were md_0_1.cpt, md_0_1_prev.cpt and >>>>> md_0_1.xtc. >>>>> Why has it happened ? I have checked log files but not able to infer a >>>>> proper answer. >>>>> >>>>> The file names are contained within the .cpt file, and those are what >>>> will be written. You haven't said what your previous command was, but >>>> the >>>> use of -deffnm makes this much easier: >>>> >>>> gmx mdrun -deffnm md_0_1 -cpi >>>> >>>> You will always get clearly named files. >>>> >>>> If its not appened, will the final trajectory .xtc obtained cover the >>>> >>>>> whole >>>>> simmulation or I ll have to combine both results? >>>>> >>>>> Use gmx check. >>>> >>>> -Justin >>>> >>>> >>>> Regards >>>> >>>>> >>>>> On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul <jalem...@vt.edu> >>>>> wrote: >>>>> >>>>> >>>>> On 5/11/18 10:42 AM, neelam wafa wrote: >>>>>> >>>>>> Dear Sir Justin! >>>>>> >>>>>>> I have restarted the simmulation but its producing a separate log >>>>>>> file >>>>>>> starting from the step where restarted. Is it normal response or >>>>>>> there >>>>>>> is >>>>>>> some problem with my restart? >>>>>>> >>>>>>> That shouldn't happen; everything should be appended unless there was >>>>>>> >>>>>> some >>>>>> problem (check the .log file itself and stdout/stderr for messages). >>>>>> Appending is for convenience but there is no functional requirement >>>>>> for >>>>>> it >>>>>> (I never append on the fly by personal preference, I just concatenate >>>>>> later). >>>>>> >>>>>> -Justin >>>>>> >>>>>> >>>>>> Thanks in advance. >>>>>> >>>>>> On Fri, May 11, 2018 at 12:06 PM, neelam wafa <neelam.w...@gmail.com> >
Re: [gmx-users] Restarting crashed simmulation.
*This is the message of gmx check for both the trajectories. I*t means that trajectory is not continuous. Am I right? *gmx check -f md_0_1.xtc* Checking file md_0_1.xtc Reading frame 0 time0.000 # Atoms 67864 Precision 0.001 (nm) Reading frame 200 time 2000.000 Item#frames Timestep (ps) Step 27310 Time 27310 Lambda 0 Coords 27310 Velocities 0 Forces 0 Box27310 * gmx check -f traj_comp.xtc* Checking file traj_comp.xtc Reading frame 0 time 2720.000 # Atoms 67864 Precision 0.001 (nm) Last frame 13 time 2850.000 Item#frames Timestep (ps) Step1410 Time1410 Lambda 0 Coords 1410 Velocities 0 Forces 0 Box 1410 On Fri, May 11, 2018 at 5:12 PM, neelam wafa <neelam.w...@gmail.com> wrote: > The previous command was : > > gmx mdrun -deffnm md_0_1 > > I didn't ust -cpi falg . > > On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 5/11/18 12:52 PM, neelam wafa wrote: >> >>> I used this command: >>> gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt >>> >>> But I think its not appending as new files are being generated with names >>> state.cpt, state_prev.cpt and traj_comp.xtc >>> while the previous files were md_0_1.cpt, md_0_1_prev.cpt and md_0_1.xtc. >>> Why has it happened ? I have checked log files but not able to infer a >>> proper answer. >>> >> >> The file names are contained within the .cpt file, and those are what >> will be written. You haven't said what your previous command was, but the >> use of -deffnm makes this much easier: >> >> gmx mdrun -deffnm md_0_1 -cpi >> >> You will always get clearly named files. >> >> If its not appened, will the final trajectory .xtc obtained cover the >>> whole >>> simmulation or I ll have to combine both results? >>> >> >> Use gmx check. >> >> -Justin >> >> >> Regards >>> >>> >>> On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> On 5/11/18 10:42 AM, neelam wafa wrote: >>>> >>>> Dear Sir Justin! >>>>> >>>>> I have restarted the simmulation but its producing a separate log file >>>>> starting from the step where restarted. Is it normal response or there >>>>> is >>>>> some problem with my restart? >>>>> >>>>> That shouldn't happen; everything should be appended unless there was >>>> some >>>> problem (check the .log file itself and stdout/stderr for messages). >>>> Appending is for convenience but there is no functional requirement for >>>> it >>>> (I never append on the fly by personal preference, I just concatenate >>>> later). >>>> >>>> -Justin >>>> >>>> >>>> Thanks in advance. >>>> >>>>> On Fri, May 11, 2018 at 12:06 PM, neelam wafa <neelam.w...@gmail.com> >>>>> wrote: >>>>> >>>>> Thanks Sir Justin! >>>>> >>>>>> I have continued the simmulation from the last step. >>>>>> >>>>>> Regards >>>>>> >>>>>> On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul <jalem...@vt.edu> >>>>>> wrote: >>>>>> >>>>>> >>>>>> On 5/10/18 7:08 AM, neelam wafa wrote: >>>>>>> >>>>>>> Hi gmx users! >>>>>>> >>>>>>>> I am running a 5ns md simmulation of a protein with 250 steps. >>>>>>>> It >>>>>>>> crashed at 136 steps due to some power problem. Now I want to >>>>>>>> continue >>>>>>>> this simmulation. In the manual following command is given: >>>>>>>> >>>>>>>> mdrun -s topol.tpr -cpi state.cpt >>>>>>>> >>>>>>>> but I am confused which file is state.cpt. I have got two cpt files >>>>>>>> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used? >>>>>>>> >>>>>>>> Look at the time stamps of the files and inspect their contents with >>>>>>>> >>>>>>> gmx >>>>&g
Re: [gmx-users] Restarting crashed simmulation.
The previous command was : gmx mdrun -deffnm md_0_1 I didn't ust -cpi falg . On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/11/18 12:52 PM, neelam wafa wrote: > >> I used this command: >> gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt >> >> But I think its not appending as new files are being generated with names >> state.cpt, state_prev.cpt and traj_comp.xtc >> while the previous files were md_0_1.cpt, md_0_1_prev.cpt and md_0_1.xtc. >> Why has it happened ? I have checked log files but not able to infer a >> proper answer. >> > > The file names are contained within the .cpt file, and those are what will > be written. You haven't said what your previous command was, but the use of > -deffnm makes this much easier: > > gmx mdrun -deffnm md_0_1 -cpi > > You will always get clearly named files. > > If its not appened, will the final trajectory .xtc obtained cover the whole >> simmulation or I ll have to combine both results? >> > > Use gmx check. > > -Justin > > > Regards >> >> >> On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> On 5/11/18 10:42 AM, neelam wafa wrote: >>> >>> Dear Sir Justin! >>>> >>>> I have restarted the simmulation but its producing a separate log file >>>> starting from the step where restarted. Is it normal response or there >>>> is >>>> some problem with my restart? >>>> >>>> That shouldn't happen; everything should be appended unless there was >>> some >>> problem (check the .log file itself and stdout/stderr for messages). >>> Appending is for convenience but there is no functional requirement for >>> it >>> (I never append on the fly by personal preference, I just concatenate >>> later). >>> >>> -Justin >>> >>> >>> Thanks in advance. >>> >>>> On Fri, May 11, 2018 at 12:06 PM, neelam wafa <neelam.w...@gmail.com> >>>> wrote: >>>> >>>> Thanks Sir Justin! >>>> >>>>> I have continued the simmulation from the last step. >>>>> >>>>> Regards >>>>> >>>>> On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul <jalem...@vt.edu> >>>>> wrote: >>>>> >>>>> >>>>> On 5/10/18 7:08 AM, neelam wafa wrote: >>>>>> >>>>>> Hi gmx users! >>>>>> >>>>>>> I am running a 5ns md simmulation of a protein with 250 steps. It >>>>>>> crashed at 136 steps due to some power problem. Now I want to >>>>>>> continue >>>>>>> this simmulation. In the manual following command is given: >>>>>>> >>>>>>> mdrun -s topol.tpr -cpi state.cpt >>>>>>> >>>>>>> but I am confused which file is state.cpt. I have got two cpt files >>>>>>> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used? >>>>>>> >>>>>>> Look at the time stamps of the files and inspect their contents with >>>>>>> >>>>>> gmx >>>>>> check. You will see an obvious difference in what they contain. Also >>>>>> consult the mdrun help info, which specifically addresses your >>>>>> question. >>>>>> >>>>>> Also I did not get a md_1_0.gro file/ Is is due to incomplete >>>>>> simmulation? >>>>>> Yes, because that file is only produced from the last step. >>>>>> >>>>>> Also do I need to specify -append flag or not? I am using version >>>>>> 5.1.5 >>>>>> -append has been the default option for many years. Again, see the >>>>>> mdrun >>>>>> help description. >>>>>> >>>>>> -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 >>>
Re: [gmx-users] Restarting crashed simmulation.
I used this command: gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt But I think its not appending as new files are being generated with names state.cpt, state_prev.cpt and traj_comp.xtc while the previous files were md_0_1.cpt, md_0_1_prev.cpt and md_0_1.xtc. Why has it happened ? I have checked log files but not able to infer a proper answer. If its not appened, will the final trajectory .xtc obtained cover the whole simmulation or I ll have to combine both results? Regards On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/11/18 10:42 AM, neelam wafa wrote: > >> Dear Sir Justin! >> >> I have restarted the simmulation but its producing a separate log file >> starting from the step where restarted. Is it normal response or there is >> some problem with my restart? >> > > That shouldn't happen; everything should be appended unless there was some > problem (check the .log file itself and stdout/stderr for messages). > Appending is for convenience but there is no functional requirement for it > (I never append on the fly by personal preference, I just concatenate > later). > > -Justin > > > Thanks in advance. >> >> On Fri, May 11, 2018 at 12:06 PM, neelam wafa <neelam.w...@gmail.com> >> wrote: >> >> Thanks Sir Justin! >>> I have continued the simmulation from the last step. >>> >>> Regards >>> >>> On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> On 5/10/18 7:08 AM, neelam wafa wrote: >>>> >>>> Hi gmx users! >>>>> >>>>> I am running a 5ns md simmulation of a protein with 250 steps. It >>>>> crashed at 136 steps due to some power problem. Now I want to >>>>> continue >>>>> this simmulation. In the manual following command is given: >>>>> >>>>> mdrun -s topol.tpr -cpi state.cpt >>>>> >>>>> but I am confused which file is state.cpt. I have got two cpt files >>>>> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used? >>>>> >>>>> Look at the time stamps of the files and inspect their contents with >>>> gmx >>>> check. You will see an obvious difference in what they contain. Also >>>> consult the mdrun help info, which specifically addresses your question. >>>> >>>> Also I did not get a md_1_0.gro file/ Is is due to incomplete >>>> simmulation? >>>> Yes, because that file is only produced from the last step. >>>> >>>> Also do I need to specify -append flag or not? I am using version 5.1.5 >>>> -append has been the default option for many years. Again, see the mdrun >>>> help description. >>>> >>>> -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. >>>> >>>> >>> > -- > == > > 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. > -- 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] Restarting crashed simmulation.
Dear Sir Justin! I have restarted the simmulation but its producing a separate log file starting from the step where restarted. Is it normal response or there is some problem with my restart? Thanks in advance. On Fri, May 11, 2018 at 12:06 PM, neelam wafa <neelam.w...@gmail.com> wrote: > Thanks Sir Justin! > I have continued the simmulation from the last step. > > Regards > > On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 5/10/18 7:08 AM, neelam wafa wrote: >> >>> Hi gmx users! >>> >>> I am running a 5ns md simmulation of a protein with 250 steps. It >>> crashed at 136 steps due to some power problem. Now I want to >>> continue >>> this simmulation. In the manual following command is given: >>> >>> mdrun -s topol.tpr -cpi state.cpt >>> >>> but I am confused which file is state.cpt. I have got two cpt files >>> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used? >>> >> >> Look at the time stamps of the files and inspect their contents with gmx >> check. You will see an obvious difference in what they contain. Also >> consult the mdrun help info, which specifically addresses your question. >> >> Also I did not get a md_1_0.gro file/ Is is due to incomplete simmulation? >>> >> >> Yes, because that file is only produced from the last step. >> >> Also do I need to specify -append flag or not? I am using version 5.1.5 >>> >> >> -append has been the default option for many years. Again, see the mdrun >> help description. >> >> -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. >> > > -- 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] Restarting crashed simmulation.
Thanks Sir Justin! I have continued the simmulation from the last step. Regards On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/10/18 7:08 AM, neelam wafa wrote: > >> Hi gmx users! >> >> I am running a 5ns md simmulation of a protein with 250 steps. It >> crashed at 136 steps due to some power problem. Now I want to >> continue >> this simmulation. In the manual following command is given: >> >> mdrun -s topol.tpr -cpi state.cpt >> >> but I am confused which file is state.cpt. I have got two cpt files >> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used? >> > > Look at the time stamps of the files and inspect their contents with gmx > check. You will see an obvious difference in what they contain. Also > consult the mdrun help info, which specifically addresses your question. > > Also I did not get a md_1_0.gro file/ Is is due to incomplete simmulation? >> > > Yes, because that file is only produced from the last step. > > Also do I need to specify -append flag or not? I am using version 5.1.5 >> > > -append has been the default option for many years. Again, see the mdrun > help description. > > -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. > -- 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] Restarting crashed simmulation.
Hi gmx users! I am running a 5ns md simmulation of a protein with 250 steps. It crashed at 136 steps due to some power problem. Now I want to continue this simmulation. In the manual following command is given: mdrun -s topol.tpr -cpi state.cpt but I am confused which file is state.cpt. I have got two cpt files md_1_0.cpt and md_1_0_prev.cpt. which one is to be used? Also I did not get a md_1_0.gro file/ Is is due to incomplete simmulation? Also do I need to specify -append flag or not? I am using version 5.1.5 Please need urgent answer. Regards Neelam Wafa -- 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] changing the time frame for simmulation
okay got it. with dt =2fs250 nsteps are for 5 ns simmulation. On Thu, 12 Apr 2018 10:35 pm Justin Lemkul, <jalem...@vt.edu> wrote: > > > On 4/12/18 1:33 PM, neelam wafa wrote: > > Thank you sir justin. > > I am confused a bit. Kindly tell me which one of the following is right > for > > 5 ns. > > nsteps =500; 500=5000 ps (5ns) > > > > or > > > > nsteps = 250 ; 2*250= 5000 ps (5ns). > > Depends on dt. Please consider what the units are. This is a trivial > calculation and is actually explained exactly in the comment field of > the file you posted previously (and in the tutorial from which you got > the file). > > -Justin > > > On Thu, 12 Apr 2018 10:13 pm Justin Lemkul, <jalem...@vt.edu> wrote: > > > >> > >> On 4/12/18 4:11 AM, neelam wafa wrote: > >>> Dear gmx users, > >>> > >>> I have run the md simmulation of my protein ligand complex for 1ns > >>> following the conditions used in tutorial by sir Justin. Now I want to > >> run > >>> the simmulations for 5ns and 10 ns. How have set it like this: > >>> integrator = md; leap-frog integrator > >>> nsteps = 500; 2 * 500 = 1 ps (10 ns) > >>> dt = 0.002 ; 2 fs > >>> > >>> Is it right? > >> Yes. > >> > >>> Is it needed to change the output control as well. It is in this form > >>>Output control > >>> nstxout = 0 ; suppress .trr output > >>> nstvout = 0 ; suppress .trr output > >>> nstenergy = 5000 ; save energies every 10.0 ps > >>> nstlog = 5000 ; update log file every 10.0 ps > >>> nstxout-compressed = 5000 ; write .xtc trajectory every 10.0 ps > >>> > >>> Please also guide me is it enough to run the last production md for 10 > ns > >>> with the npt and nvt run unchanged or I have change the time frame of > the > >>> equliberation steps as well. > >> You do not need to change the amount of equilibration. > >> > >>> Further how can I set the parameters for a 5ns simmulation? > >> It's the same math that you did above. > >> > >> -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. > >> > > -- > == > > 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. > -- 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] changing the time frame for simmulation
Thank you sir justin. I am confused a bit. Kindly tell me which one of the following is right for 5 ns. nsteps =500; 500=5000 ps (5ns) or nsteps = 250 ; 2*250= 5000 ps (5ns). On Thu, 12 Apr 2018 10:13 pm Justin Lemkul, <jalem...@vt.edu> wrote: > > > On 4/12/18 4:11 AM, neelam wafa wrote: > > Dear gmx users, > > > > I have run the md simmulation of my protein ligand complex for 1ns > > following the conditions used in tutorial by sir Justin. Now I want to > run > > the simmulations for 5ns and 10 ns. How have set it like this: > > integrator = md; leap-frog integrator > > nsteps = 500; 2 * 500 = 1 ps (10 ns) > > dt = 0.002 ; 2 fs > > > > Is it right? > > Yes. > > > Is it needed to change the output control as well. It is in this form > > Output control > > nstxout = 0 ; suppress .trr output > > nstvout = 0 ; suppress .trr output > > nstenergy = 5000 ; save energies every 10.0 ps > > nstlog = 5000 ; update log file every 10.0 ps > > nstxout-compressed = 5000 ; write .xtc trajectory every 10.0 ps > > > > Please also guide me is it enough to run the last production md for 10 ns > > with the npt and nvt run unchanged or I have change the time frame of the > > equliberation steps as well. > > You do not need to change the amount of equilibration. > > > Further how can I set the parameters for a 5ns simmulation? > > It's the same math that you did above. > > -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. > -- 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] changing the time frame for simmulation
Dear gmx users, I have run the md simmulation of my protein ligand complex for 1ns following the conditions used in tutorial by sir Justin. Now I want to run the simmulations for 5ns and 10 ns. How have set it like this: integrator = md; leap-frog integrator nsteps = 500; 2 * 500 = 1 ps (10 ns) dt = 0.002 ; 2 fs Is it right? Is it needed to change the output control as well. It is in this form Output control nstxout = 0 ; suppress .trr output nstvout = 0 ; suppress .trr output nstenergy = 5000 ; save energies every 10.0 ps nstlog = 5000 ; update log file every 10.0 ps nstxout-compressed = 5000 ; write .xtc trajectory every 10.0 ps Please also guide me is it enough to run the last production md for 10 ns with the npt and nvt run unchanged or I have change the time frame of the equliberation steps as well. Further how can I set the parameters for a 5ns simmulation? Thanks in advance. Regards -- 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] problem in running job.sh for free energy calculations.
Thanks sir Mark and Justin. I ll try to figure it out with the administer. But in case the problem is not resolved, is it okay if I run the commands directly through terminal? Will it effect the results? I know it ll be a tedious job. Regards Neelam Wafa On Mon, 9 Apr 2018 10:03 pm Justin Lemkul, <jalem...@vt.edu> wrote: > > > On 4/9/18 12:56 PM, neelam wafa wrote: > > Thanks Sir for your quick response. > > These are the errors I am getting. > > Error in user input: > > Invalid command-line options > >In command-line option -f > > File '/home/Downloads/Free_Energy/MDP/EM/em_steep_0.mdp' does not > exist > > or > > is not accessible. > >In command-line option -c > > File '/home/Downloads/Free_Energy/Methane/methane_water.gro' does > not > > exist or is not accessible. > >In command-line option -p > > File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist > or > > is > > not accessible. > > job.sh: line 30: mdrun: command not found > > > > > > Error in user input: > > Invalid command-line options > >In command-line option -f > > File '/home/Downloads/Free_Energy/MDP/NVT/nvt_0.mdp' does not exist > or > > is > > not accessible. > >In command-line option -p > > File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist > or > > is > > not accessible. > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > --- > > job.sh: line 65: mdrun: command not found > > > > similar errors I get for all the sets. > > It seems that the compute node has no idea where your files or > executables are, which means however you've configured your job script > is incorrect for your cluster. Consult your system administrator, as > none of these problems are actually specific to GROMACS. > > -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. > -- 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] problem in running job.sh for free energy calculations.
Hi This is how I modified the job.sh script #!/bin/bash # Set some environment variables FREE_ENERGY=/home/Downloads/Free_Energy echo "Free energy home directory set to $FREE_ENERGY" MDP=$FREE_ENERGY/MDP echo ".mdp files are stored in $MDP" LAMBDA=0 # A new directory will be created for each value of lambda and # at each step in the workflow for maximum organization. mkdir Lambda_$LAMBDA cd Lambda_$LAMBDA # # ENERGY MINIMIZATION 1: STEEP # # echo "Starting minimization for lambda = $LAMBDA..." mkdir EM_1 cd EM_1 # Iterative calls to grompp and mdrun to run the simulations gmx grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/Methane/methane_water.gro -p $FREE_ENERGY/Methane/topol.top -o min$LAMBDA.tpr mdrun -nt 2 -deffnm min$LAMBDA sleep 10 # # ENERGY MINIMIZATION 2: L-BFGS # # cd ../ mkdir EM_2 cd EM_2 # We use -maxwarn 1 here because grompp incorrectly complains about use of a plain cutoff; this is a minor issue # that will be fixed in a future version of Gromacs gmx grompp -f $MDP/EM/em_l-bfgs_$LAMBDA.mdp -c ../EM_1/min$LAMBDA.gro -p $FREE_ENERGY/Methane/topol.top -o min$LAMBDA.tpr -maxwarn 1 # Run L-BFGS in serial (cannot be run in parallel) mdrun -nt 1 -deffnm min$LAMBDA echo "Minimization complete." sleep 10 # # NVT EQUILIBRATION # # echo "Starting constant volume equilibration..." cd ../ mkdir NVT cd NVT gmx grompp -f $MDP/NVT/nvt_$LAMBDA.mdp -c ../EM_2/min$LAMBDA.gro -p $FREE_ENERGY/Methane/topol.top -o nvt$LAMBDA.tpr mdrun -nt 2 -deffnm nvt$LAMBDA echo "Constant volume equilibration complete." sleep 10 # # NPT EQUILIBRATION # # echo "Starting constant pressure equilibration..." cd ../ mkdir NPT cd NPT gmx grompp -f $MDP/NPT/npt_$LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p $FREE_ENERGY/Methane/topol.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr mdrun -nt 2 -deffnm npt$LAMBDA echo "Constant pressure equilibration complete." sleep 10 # # PRODUCTION MD # # echo "Starting production MD simulation..." cd ../ mkdir Production_MD cd Production_MD gmx grompp -f $MDP/Production_MD/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p $FREE_ENERGY/Methane/topol.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr mdrun -nt 2 -deffnm md$LAMBDA echo "Production MD complete." # End echo "Ending. Job completed for lambda = $LAMBDA" On Mon, Apr 9, 2018 at 4:56 PM, neelam wafa <neelam.w...@gmail.com> wrote: > Thanks Sir for your quick response. > These are the errors I am getting. > Error in user input: > Invalid command-line options > In command-line option -f > File '/home/Downloads/Free_Energy/MDP/EM/em_steep_0.mdp' does not > exist or > is not accessible. > In command-line option -c > File '/home/Downloads/Free_Energy/Methane/methane_water.gro' does not > exist or is not accessible. > In command-line option -p > File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist > or is > not accessible. > job.sh: line 30: mdrun: command not found > > > Error in user input: > Invalid command-line options > In command-line option -f > File '/home/Downloads/Free_Energy/MDP/NVT/nvt_0.mdp' does not exist > or is > not accessible. > In command-line option -p > File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist > or is > not accessible. > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > job.sh: line 65: mdrun: command not found > > similar errors I get for all the sets. > > Regards > Neelam Wafa > > > > > On Mon, Apr 9, 2018 at 3:30 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 4/9/18 11:25 AM, neelam wafa wrote: >> >>> Dear sir Justin >>> >>> I am doing your tutorial of free energy calculations for methane in >>> water. >>> I have created the .mdp and .sh files using the perl script you >>> provided. >>> I have also made the FREE_ENERGY and MDP directories as in the job. sh >>> script. gro file and topology files are also in the relevant folder but >>> when I run job.sh script with command bash job.sh, it says the files the >>> .mdp file, the methane_water.gro file and topol.top file either dont >>> exist >>> or not accessible. I have checked the files are in their proper places >>> and >>> are searched on terminal and opened t
Re: [gmx-users] problem in running job.sh for free energy calculations.
Thanks Sir for your quick response. These are the errors I am getting. Error in user input: Invalid command-line options In command-line option -f File '/home/Downloads/Free_Energy/MDP/EM/em_steep_0.mdp' does not exist or is not accessible. In command-line option -c File '/home/Downloads/Free_Energy/Methane/methane_water.gro' does not exist or is not accessible. In command-line option -p File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist or is not accessible. job.sh: line 30: mdrun: command not found Error in user input: Invalid command-line options In command-line option -f File '/home/Downloads/Free_Energy/MDP/NVT/nvt_0.mdp' does not exist or is not accessible. In command-line option -p File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist or is not accessible. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- job.sh: line 65: mdrun: command not found similar errors I get for all the sets. Regards Neelam Wafa On Mon, Apr 9, 2018 at 3:30 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/9/18 11:25 AM, neelam wafa wrote: > >> Dear sir Justin >> >> I am doing your tutorial of free energy calculations for methane in water. >> I have created the .mdp and .sh files using the perl script you >> provided. >> I have also made the FREE_ENERGY and MDP directories as in the job. sh >> script. gro file and topology files are also in the relevant folder but >> when I run job.sh script with command bash job.sh, it says the files the >> .mdp file, the methane_water.gro file and topol.top file either dont exist >> or not accessible. I have checked the files are in their proper places and >> are searched on terminal and opened though comand with vi editor. I have >> also given chmod 777 permission to these files. but no way out of the >> problem. please help me out. I have been searching the archive and google >> for the last three days but could not sort out. When i run the grompp and >> gmx md run commands directly through the terminal it works but not through >> the job.sh. >> Please suggest me a solution. Sorry for the long text or for addressing >> directly to you. >> > > Without specific error messages, I have nothing to go on to suggest a > solution. Perhaps you should be consulting your system administrator if the > commands are syntactically valid but not operational in the queued > environment. > > -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. > -- 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] problem in running job.sh for free energy calculations.
Dear sir Justin I am doing your tutorial of free energy calculations for methane in water. I have created the .mdp and .sh files using the perl script you provided. I have also made the FREE_ENERGY and MDP directories as in the job. sh script. gro file and topology files are also in the relevant folder but when I run job.sh script with command bash job.sh, it says the files the .mdp file, the methane_water.gro file and topol.top file either dont exist or not accessible. I have checked the files are in their proper places and are searched on terminal and opened though comand with vi editor. I have also given chmod 777 permission to these files. but no way out of the problem. please help me out. I have been searching the archive and google for the last three days but could not sort out. When i run the grompp and gmx md run commands directly through the terminal it works but not through the job.sh. Please suggest me a solution. Sorry for the long text or for addressing directly to you. Thanks in advance. Regards Neelam wafa -- 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] creating topology for ligand
ok thanks. On 2 Mar 2018 22:25, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > On 3/2/18 12:18 PM, neelam wafa wrote: > >> Thanks Justin >> >> Can you please suggest me any article or reading that can help me to >> understand the factors to be considered while choosing a force field or to >> parameterize the ligand? >> > > I could suggest hundreds. Start with even a basic Google search for MD > force field review papers, references in the GROMACS manual for each of the > force fields, etc. > > -Justin > > On 1 Mar 2018 18:14, "Justin Lemkul" <jalem...@vt.edu> wrote: >> >> >>> On 3/1/18 8:03 AM, neelam wafa wrote: >>> >>> Dear gmx users >>>> >>>> I am trying to run a protein ligand simmulation. How can i create >>>> topolgy >>>> for ligand. prodrg topology is not reliable then which server or >>>> software >>>> can be used? can topology be created by T LEEP off ambertools package >>>> for >>>> gromacs?? >>>> >>>> The method you use depends on the parent force field you've chosen. The >>> PRODRG and ATB servers are for GROMOS force fields, GAFF methods (RED >>> server, antechamber, etc) are for AMBER. ParamChem/CGenFF are for CHARMM. >>> You can't mix and match. You need to do your homework here to make sure >>> that the force field you've chosen for your protein is an appropriate >>> model, as well as whether or not you can feasibly parametrize your ligand >>> (not an easy task and generally not advisable for a beginner, because you >>> should *never* trust a black box and always validate the topology in a >>> manner consistent with the parent force field). >>> >>> secondly how to select the boxtype as I am new to simmulation so cant fix >>> >>>> the problem. Please also guide me what factors should be considered to >>>> select the water model?? >>>> >>>> The water model is part of the force field; each has been parametrized >>> with a particular model (though some do show some insensitivity if >>> changed, >>> but again this is your homework to do before ever thinking about doing >>> anything in GROMACS or any other MD engine). >>> >>> The box shape has no effect as long as you set up a suitable box-solute >>> distance that satisfies the minimum image convention. You can use >>> non-cubic >>> boxes to speed up the simulation if it's just a simple protein (complex) >>> in >>> water. >>> >>> -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.biochem.vt.edu/people/faculty/JustinLemkul.html >>> >>> == >>> >>> -- >>> 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. >>> >>> > -- > == > > 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.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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] atom naming needs to be considered.
I am trying md simmulation of a protein kinase and ligand to check the stability of the protein ligand complex formed. On 2 Mar 2018 22:22, "Mark Abraham" <mark.j.abra...@gmail.com> wrote: > Hi, > > We can't tell there's a problem because we know nothing about what you are > trying to do except it involves pdb2gmx > > Mark > > On Fri, Mar 2, 2018, 18:15 neelam wafa <neelam.w...@gmail.com> wrote: > > > Is there any way to fix this problem with the start and end terminals? > > > > On 2 Mar 2018 22:12, "neelam wafa" <neelam.w...@gmail.com> wrote: > > > > > Thanks dear > > > > > > So it means I can continue with rest of the process. Will it not effect > > > the results? > > > > > > On 1 Mar 2018 19:53, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > > > > > > > > > > On 3/1/18 9:35 AM, neelam wafa wrote: > > > > > >> Hi! > > >> Dear all I am running pdb2gmx command to create the protein topology > but > > >> getting this error. please guide me how to fix this problem. > > >> > > >> WARNING: WARNING: Residue 1 named TRP of a molecule in the input file > > was > > >> mapped > > >> to an entry in the topology database, but the atom H used in > > >> an interaction of type angle in that entry is not found in the > > >> input file. Perhaps your atom and/or residue naming needs to be > > >> fixed. > > >> > > >> > > >> > > >> WARNING: WARNING: Residue 264 named ASN of a molecule in the input > file > > >> was > > >> mapped > > >> to an entry in the topology database, but the atom O used in > > >> an interaction of type angle in that entry is not found in the > > >> input file. Perhaps your atom and/or residue naming needs to be > > >> fixed. > > >> > > > > > > Neither of those is an error (warnings, notes, and errors are all > > > different in GROMACS), and correspond to normal output when patching N- > > and > > > C-termini due to the deletion of atoms. > > > > > > -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.biochem.vt.edu/people/faculty/JustinLemkul.html > > > > > > == > > > > > > -- > > > 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. > > > -- > 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] creating topology for ligand
Thanks Justin Can you please suggest me any article or reading that can help me to understand the factors to be considered while choosing a force field or to parameterize the ligand? On 1 Mar 2018 18:14, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > On 3/1/18 8:03 AM, neelam wafa wrote: > >> Dear gmx users >> >> I am trying to run a protein ligand simmulation. How can i create topolgy >> for ligand. prodrg topology is not reliable then which server or software >> can be used? can topology be created by T LEEP off ambertools package for >> gromacs?? >> > > The method you use depends on the parent force field you've chosen. The > PRODRG and ATB servers are for GROMOS force fields, GAFF methods (RED > server, antechamber, etc) are for AMBER. ParamChem/CGenFF are for CHARMM. > You can't mix and match. You need to do your homework here to make sure > that the force field you've chosen for your protein is an appropriate > model, as well as whether or not you can feasibly parametrize your ligand > (not an easy task and generally not advisable for a beginner, because you > should *never* trust a black box and always validate the topology in a > manner consistent with the parent force field). > > secondly how to select the boxtype as I am new to simmulation so cant fix >> the problem. Please also guide me what factors should be considered to >> select the water model?? >> > > The water model is part of the force field; each has been parametrized > with a particular model (though some do show some insensitivity if changed, > but again this is your homework to do before ever thinking about doing > anything in GROMACS or any other MD engine). > > The box shape has no effect as long as you set up a suitable box-solute > distance that satisfies the minimum image convention. You can use non-cubic > boxes to speed up the simulation if it's just a simple protein (complex) in > water. > > -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.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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] atom naming needs to be considered.
Is there any way to fix this problem with the start and end terminals? On 2 Mar 2018 22:12, "neelam wafa" <neelam.w...@gmail.com> wrote: > Thanks dear > > So it means I can continue with rest of the process. Will it not effect > the results? > > On 1 Mar 2018 19:53, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > > On 3/1/18 9:35 AM, neelam wafa wrote: > >> Hi! >> Dear all I am running pdb2gmx command to create the protein topology but >> getting this error. please guide me how to fix this problem. >> >> WARNING: WARNING: Residue 1 named TRP of a molecule in the input file was >> mapped >> to an entry in the topology database, but the atom H used in >> an interaction of type angle in that entry is not found in the >> input file. Perhaps your atom and/or residue naming needs to be >> fixed. >> >> >> >> WARNING: WARNING: Residue 264 named ASN of a molecule in the input file >> was >> mapped >> to an entry in the topology database, but the atom O used in >> an interaction of type angle in that entry is not found in the >> input file. Perhaps your atom and/or residue naming needs to be >> fixed. >> > > Neither of those is an error (warnings, notes, and errors are all > different in GROMACS), and correspond to normal output when patching N- and > C-termini due to the deletion of atoms. > > -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.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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] atom naming needs to be considered.
Thanks dear So it means I can continue with rest of the process. Will it not effect the results? On 1 Mar 2018 19:53, "Justin Lemkul" <jalem...@vt.edu> wrote: On 3/1/18 9:35 AM, neelam wafa wrote: > Hi! > Dear all I am running pdb2gmx command to create the protein topology but > getting this error. please guide me how to fix this problem. > > WARNING: WARNING: Residue 1 named TRP of a molecule in the input file was > mapped > to an entry in the topology database, but the atom H used in > an interaction of type angle in that entry is not found in the > input file. Perhaps your atom and/or residue naming needs to be > fixed. > > > > WARNING: WARNING: Residue 264 named ASN of a molecule in the input file was > mapped > to an entry in the topology database, but the atom O used in > an interaction of type angle in that entry is not found in the > input file. Perhaps your atom and/or residue naming needs to be > fixed. > Neither of those is an error (warnings, notes, and errors are all different in GROMACS), and correspond to normal output when patching N- and C-termini due to the deletion of atoms. -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.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] atom naming needs to be considered.
Hi! Dear all I am running pdb2gmx command to create the protein topology but getting this error. please guide me how to fix this problem. WARNING: WARNING: Residue 1 named TRP of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 264 named ASN of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Regards -- 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] creating topology for ligand
Dear gmx users I am trying to run a protein ligand simmulation. How can i create topolgy for ligand. prodrg topology is not reliable then which server or software can be used? can topology be created by T LEEP off ambertools package for gromacs?? secondly how to select the boxtype as I am new to simmulation so cant fix the problem. Please also guide me what factors should be considered to select the water model?? Thanks in advance. -- 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] PROBLEM IN COORDINATES
thanks. problem resolved. On 21 Feb 2018 08:13, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > On 2/20/18 9:50 PM, neelam wafa wrote: > >> Dear gmx users >> >> I am still stuck at this point. >> error obtained is this >> Fatal error: >> number of coordinates in coordinate file (solv.gro, 32803) >> does not match topology (topol.top, 32818) >> There is a difference of 15. I think its not considering the ligand as 15 >> is i think for ligand. the ligand. the entries of ligand in gro file are >> these. >> 15 >> 1JZ4 C4 1 2.946 -2.601 0.141 >> 1JZ4 C14 2 3.009 -2.568 0.005 >> 1JZ4 C13 3 2.965 -2.664 -0.107 >> 1JZ4 C12 4 2.834 -2.642 -0.154 >> 1JZ4 C11 5 2.734 -2.734 -0.116 >> 1JZ4 H11 6 2.753 -2.810 -0.040 >> 1JZ4 C7 7 2.606 -2.727 -0.176 >> 1JZ4 H7 8 2.529 -2.798 -0.147 >> 1JZ4 C8 9 2.578 -2.628 -0.273 >> 1JZ4 H8 10 2.479 -2.624 -0.319 >> 1JZ4 C9 11 2.677 -2.536 -0.311 >> 1JZ4 H9 12 2.655 -2.460 -0.387 >> 1JZ4 C10 13 2.804 -2.543 -0.251 >> 1JZ4 OAB 14 2.900 -2.451 -0.285 >> 1JZ4 HAB 15 2.863 -2.389 -0.354 >> 0.68000 0.68000 0.68000 >> >> Help me out please. >> > > Looks like you probably didn't copy the ligand coordinates into the > topology. The topology thinks it's there and the coordinates say it's not. > The solution to this error is always the same: proper bookkeeping. > > -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.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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] PROBLEM IN COORDINATES
Dear gmx users I am still stuck at this point. error obtained is this Fatal error: number of coordinates in coordinate file (solv.gro, 32803) does not match topology (topol.top, 32818) There is a difference of 15. I think its not considering the ligand as 15 is i think for ligand. the ligand. the entries of ligand in gro file are these. 15 1JZ4 C4 1 2.946 -2.601 0.141 1JZ4 C14 2 3.009 -2.568 0.005 1JZ4 C13 3 2.965 -2.664 -0.107 1JZ4 C12 4 2.834 -2.642 -0.154 1JZ4 C11 5 2.734 -2.734 -0.116 1JZ4 H11 6 2.753 -2.810 -0.040 1JZ4 C7 7 2.606 -2.727 -0.176 1JZ4 H7 8 2.529 -2.798 -0.147 1JZ4 C8 9 2.578 -2.628 -0.273 1JZ4 H8 10 2.479 -2.624 -0.319 1JZ4 C9 11 2.677 -2.536 -0.311 1JZ4 H9 12 2.655 -2.460 -0.387 1JZ4 C10 13 2.804 -2.543 -0.251 1JZ4 OAB 14 2.900 -2.451 -0.285 1JZ4 HAB 15 2.863 -2.389 -0.354 0.68000 0.68000 0.68000 Help me out please. Regards On Sun, Feb 18, 2018 at 6:45 PM, Alex <nedoma...@gmail.com> wrote: > Hi, > > The error is informative. Check the number of entries in the gro file and > compare it with the [ atoms ] section in your topology, together with > anything that's added under [ system ]. The total numbers need to match. > > Alex > > > > On 2/18/2018 11:34 AM, neelam wafa wrote: > >> Dear gmx users, >> >> I am doing the tutorial of protein ligand simmulation given at >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx >> -tutorials/com. >> when I give following command, I get an error. >> >> gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr >> >> the error says the number of coordinates in the sol.gro file and >> topol.top file does not match. How to fix it. >> >> Help me out please. >> >> Thanks in advance. >> >> Regards >> > > -- > 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] PROBLEM IN COORDINATES
Dear gmx users, I am doing the tutorial of protein ligand simmulation given at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/com. when I give following command, I get an error. gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr the error says the number of coordinates in the sol.gro file and topol.top file does not match. How to fix it. Help me out please. Thanks in advance. Regards -- 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] Fwd: how to get .mdp files
-- Forwarded message -- From: "neelam wafa" <neelam.w...@gmail.com> Date: 17 Feb 2018 00:57 Subject: how to get .mdp files To: <gromacs.org_gmx-users-ow...@maillist.sys.kth.se> Cc: Hi I am new to this list. I have run the gromacs tutorial ' lysosime in water'. now i have to run a protein ligand simmulation. But i am confused about how to generate .mdp files as in tutorial they have used five .mdp files which are to be downloaded from bevanlab.biochem. These are ions.mdp, em.mdp, nvt.mdp, npt.mdp and md.mdp. Are the same files to be used or these have to be generated with aome software according to the protein and ligand. Thanks in advance. Regards Neelam -- 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.
