[gmx-users] Protein ligand simulation topology
Respected sir/mam, While doing the simulation of my protein with a ligand I received the following error: Fatal Error: No line with moleculetype 'SOL' found in the [molecules] section of the 'topol.top' Molecule section of my topology file is as follows: [molecules] ; Compound#mols Protein_chain_A 1 AB1 1 SOL 17416 Also the number of SOL molecules in the topology file do not match with the ones shown in the terminal for selecting the continous group of solvent. In the terminal number of solvent molecules is 52248. Please help me resolve this issue. Thanking you in advance. Sincerely Deepanshu SIngla -- 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] Protein ligand simulation
Respected sir/mam, During ligand topology generation I received the following error: Please be sure to use the same version of CGenFF in your simulation that was used during parameter generation: --version of CGenFF detected in charmm36-mar2019.ff/forcefield.doc : 4.1 WARNING: cGenFF versions are not equivalent! ERROR: could not detect CGenFF version. Exiting Please help me resolve the error. Thanking you in advance. Deepanshu Singla -- 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] Protein ligand simulation
I am trying to learn protein ligand simulation. I tried to follow the steps
for lysozyme using the GROMACS tutorial. I received the following error:
*ERROR 1 {file jz4.itp, line 183]:*
* No default Proper Dih. types*
*ERROR 2 [file jz4.itp, line 194]:*
* No default Proper Dih. types*
*Fatal error: *
*Syntax error -File forcefield.itp, line 10*
*Last line resd:*
*'[defaults]'*
*Invalid order for directive defaults*
Please help me resolve this error.
Thanking you in advance.
Deepanshu Singla
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[gmx-users] Protein ligand simulation
I am trying to learn protein ligand simulation. I tried to follow the steps
for lysozyme using the GROMACS tutorial. I received the following error:
*ERROR 1 {file jz4.itp, line 183]:*
* No default Proper Dih. types*
*ERROR 2 [file jz4.itp, line 194]:*
* No default Proper Dih. types*
*Fatal error: *
*Syntax error -File forcefield.itp, line 10*
*Last line resd:*
*'{defaults]'*
*Invalid order for directive defaults*
Please help me resolve this error.
Thanking you in advance.
Deepanshu Singla
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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* 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] Reparametrization of ligan topology
> > I have generated the ligand topolgy by following the steps mentioned in > the gromacs tutorial and using charmm CGenFF. The penalty scores is more > than 50. I tried to follow the tutorial for reparameterization (available > on the MacKerell lab website). I couldn't follow the tutorial properly > because of its complex nature. I am a student trying to learn GROMACS. It will be extremely useful if someone could guide me in detail on how to optimize the parameters. I will be extremely grateful for your help. I am attaching the file for reference. -- 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] Manual reparameterization for ligand topology
I used the CGenFF program for generating the ligand topology. The GROMACS tutorial recommends the manual reparameterization of force field in case the penalty score exceeds 50. My ligand penalty scores exceed 50 and don't know how to change the parameters. Please help in this regard. I am attaching the str file of ligand generated by using the CGenFF server. Thanks, Deepanshu Singla -- 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] Using grace in windows
Thank you Mr. Micholas D. for the reply. Sir is it possible to use qtgrace by using linux subsystem command line. If so then can you please tell me the commands to do so. Deepanshu On Wed, 8 May 2019, 19:14 DEEPANSHU SINGLA, wrote: > I am trying to plot graph from gromacs generated xvg files in windows 10 > using Linux subsystem command line. I installed grace using the same > command line. When I try to plot the graph using grce in the command line > by using the following command : xmgrace filename.xvg > > > > I get the following error: > > > > Can't open display > > Failed initializing GUI, exiting > > > > Please, guide me help me in ploting the graph in windows. > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > -- 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] Using grace in windows
I am trying to plot graph from gromacs generated xvg files in windows 10 using Linux subsystem command line. I installed grace using the same command line. When I try to plot the graph using grce in the command line by using the following command : xmgrace filename.xvg I get the following error: Can't open display Failed initializing GUI, exiting Please, guide me help me in ploting the graph in windows. Sent from Mail for Windows 10 -- 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.
