[gmx-users] Adding a substrate into protein-lipid bilayer system
Dear Users, I have a protein-lipid bilayer system and this protein is an ion channel. I would like to force a substrate eg, ammonia (NH3) passing through this channel. I wonder when it is appropriate to add NH3 into the system and how to setup the control of temperature coupling in thermostats. For example, 1. add NH3 first with the protein and then embed protein-NH3 into the lipid or 2. embed the protein into lipid with an equilibration, followed by adding NH3 into the system Also, if the substrate has a charge, which order is preferred ? Thanks, Dewey -- 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] Cyclohexane simulation problem
On 5/31/15 6:00 AM, mohsen shahlaei wrote: Thank you Justin for prompt reply.I have been used coulombtype= Cut-off in my mdp file for Cyclohexane energy minimization but the results sound odd.I used cyclohexane density (0.824 g/ml) for calculating number of CHX molecules in a 10 nm3 (about 56 molecules). Then I used following command to make a box.gmx insert-molecules -ci chx.gro -nmol 56 -box 2.154434 2.154434 2.154434 -o chx_box.grochx.gro and chx.itp that I used are: =chx.itp ==; ; ; This file was generated by PRODRG version AA100323.0717 ; PRODRG written/copyrighted by Daan van Aalten ; and Alexander Schuettelkopf ; ; Questions/comments to d...@davapc1.bioch.dundee.ac.uk ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. ; ; [ moleculetype ] ; Name nrexcl chx 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH1 1 chx CAA 10.000 14.0270 2 CH1 1 chx CAB 10.000 14.0270 3 CH1 1 chx CAE 10.000 14.0270 4 CH1 1 chx CAF 10.000 14.0270 5 CH1 1 chx CAD 10.000 14.0270 6 CH1 1 chx CAC 10.000 14.0270 [ bonds ] ; ai aj fuc0, c1, ... 1 2 20.152 543.00.152 543.0 ; CAA CAB 1 6 20.152 543.00.152 543.0 ; CAA CAC 2 3 20.152 543.00.152 543.0 ; CAB CAE 3 4 20.152 543.00.152 543.0 ; CAE CAF 4 5 20.152 543.00.152 543.0 ; CAF CAD 5 6 20.152 543.00.152 543.0 ; CAD CAC [ pairs ] ; ai aj fuc0, c1, ... 1 4 1 ; CAA CAF 2 5 1 ; CAB CAD 3 6 1 ; CAE CAC [ angles ] ; ai aj ak fuc0, c1, ... 2 1 6 2109.5 520.0109.5 520.0 ; CAB CAA CAC 1 2 3 2109.5 520.0109.5 520.0 ; CAA CAB CAE 2 3 4 2109.5 520.0109.5 520.0 ; CAB CAE CAF 3 4 5 2109.5 520.0109.5 520.0 ; CAE CAF CAD 4 5 6 2109.5 520.0109.5 520.0 ; CAF CAD CAC 1 6 5 2109.5 520.0109.5 520.0 ; CAA CAC CAD [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 3 2 1 6 1 0.05.9 3 0.05.9 3 ; dih CAE CAB CAA CAC 5 6 1 2 1 0.05.9 3 0.05.9 3 ; dih CAD CAC CAA CAB 4 3 2 1 1 0.05.9 3 0.05.9 3 ; dih CAF CAE CAB CAA 5 4 3 2 1 0.05.9 3 0.05.9 3 ; dih CAD CAF CAE CAB 6 5 4 3 1 0.05.9 3 0.05.9 3 ; dih CAC CAD CAF CAE 1 6 5 4 1 0.05.9 3 0.05.9 3 ; dih CAA CAC CAD CAF =chx.gro PRODRG COORDS 6 1chx C AA1 0.155 0.105 0.177 1chx C AB2 0.100 0.247 0.184 1chx C AE3 0.182 0.344 0.100 1chx C AF4 0.330 0.339 0.137 1chx C AD5 0.385 0.196 0.130 1chx C AC6 0.303 0.100 0.214 0.48500 0.44400 0.31400=== As I suspected before, you have a malformed coordinate file. Fix it before doing anything. http://manual.gromacs.org/online/gro.html Then I minimized the energy of generated box as follows:gmx grompp -f minim.mdp -c chx_box.gro -p chx_box.top -o em.tpr -maxwarn 1gmx mdrun -deffnm em -v The warning I got in grompp runing was WARNING 1 [file chx_box.top, line 58]: 336 non-matching atom names atom names from chx_box.top will be used atom names from chx_box.gro will be ignored Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are:56 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 1005.00 This run will generate roughly 2 Mb of data There was 1 note There was 1 warning --- Program gmx, VERSION 5.0.4 Source code file: /home/mohsen/Downloads/gromacs-5.0.4/src/gromacs/gmxpreprocess/grompp.c, line: 2087 Fatal error: Too many warnings (1), gmx terminated. So I used -maxwarn 1 Generally dangerous. Perhaps not relevant here, but you shouldn't get into this habit. Fix the problems in the input rather than overriding
[gmx-users] Cyclohexane simulation problem
Thank you Justin for prompt reply.I have been used coulombtype = Cut-off in my mdp file for Cyclohexane energy minimization but the results sound odd.I used cyclohexane density (0.824 g/ml) for calculating number of CHX molecules in a 10 nm3 (about 56 molecules). Then I used following command to make a box.gmx insert-molecules -ci chx.gro -nmol 56 -box 2.154434 2.154434 2.154434 -o chx_box.grochx.gro and chx.itp that I used are: =chx.itp ==; ; ; This file was generated by PRODRG version AA100323.0717 ; PRODRG written/copyrighted by Daan van Aalten ; and Alexander Schuettelkopf ; ; Questions/comments to d...@davapc1.bioch.dundee.ac.uk ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. ; ; [ moleculetype ] ; Name nrexcl chx 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH1 1 chx CAA 1 0.000 14.0270 2 CH1 1 chx CAB 1 0.000 14.0270 3 CH1 1 chx CAE 1 0.000 14.0270 4 CH1 1 chx CAF 1 0.000 14.0270 5 CH1 1 chx CAD 1 0.000 14.0270 6 CH1 1 chx CAC 1 0.000 14.0270 [ bonds ] ; ai aj fu c0, c1, ... 1 2 2 0.152 543.0 0.152 543.0 ; CAA CAB 1 6 2 0.152 543.0 0.152 543.0 ; CAA CAC 2 3 2 0.152 543.0 0.152 543.0 ; CAB CAE 3 4 2 0.152 543.0 0.152 543.0 ; CAE CAF 4 5 2 0.152 543.0 0.152 543.0 ; CAF CAD 5 6 2 0.152 543.0 0.152 543.0 ; CAD CAC [ pairs ] ; ai aj fu c0, c1, ... 1 4 1 ; CAA CAF 2 5 1 ; CAB CAD 3 6 1 ; CAE CAC [ angles ] ; ai aj ak fu c0, c1, ... 2 1 6 2 109.5 520.0 109.5 520.0 ; CAB CAA CAC 1 2 3 2 109.5 520.0 109.5 520.0 ; CAA CAB CAE 2 3 4 2 109.5 520.0 109.5 520.0 ; CAB CAE CAF 3 4 5 2 109.5 520.0 109.5 520.0 ; CAE CAF CAD 4 5 6 2 109.5 520.0 109.5 520.0 ; CAF CAD CAC 1 6 5 2 109.5 520.0 109.5 520.0 ; CAA CAC CAD [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 3 2 1 6 1 0.0 5.9 3 0.0 5.9 3 ; dih CAE CAB CAA CAC 5 6 1 2 1 0.0 5.9 3 0.0 5.9 3 ; dih CAD CAC CAA CAB 4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih CAF CAE CAB CAA 5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih CAD CAF CAE CAB 6 5 4 3 1 0.0 5.9 3 0.0 5.9 3 ; dih CAC CAD CAF CAE 1 6 5 4 1 0.0 5.9 3 0.0 5.9 3 ; dih CAA CAC CAD CAF =chx.gro PRODRG COORDS 6 1chx C AA 1 0.155 0.105 0.177 1chx C AB 2 0.100 0.247 0.184 1chx C AE 3 0.182 0.344 0.100 1chx C AF 4 0.330 0.339 0.137 1chx C AD 5 0.385 0.196 0.130 1chx C AC 6 0.303 0.100 0.214 0.48500 0.44400 0.31400=== Then I minimized the energy of generated box as follows:gmx grompp -f minim.mdp -c chx_box.gro -p chx_box.top -o em.tpr -maxwarn 1gmx mdrun -deffnm em -v The warning I got in grompp runing was WARNING 1 [file chx_box.top, line 58]: 336 non-matching atom names atom names from chx_box.top will be used atom names from chx_box.gro will be ignored Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 56 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 1005.00 This run will generate roughly 2 Mb of data There was 1 note There was 1 warning --- Program gmx, VERSION 5.0.4 Source code file: /home/mohsen/Downloads/gromacs-5.0.4/src/gromacs/gmxpreprocess/grompp.c, line: 2087 Fatal error: Too many warnings (1), gmx terminated. So I used -maxwarn 1 The chx_box ITP is==chx_box.itp=; ; File 'topol.top' was generated ; By user: mohsen (1000) ; On host: mohsen-All-Series ; At date: Wed May 20 12:09:46 2015 ; ; This is a standalone topology file
Re: [gmx-users] regarding pdb2gmx
Thank you very much for your help Justin. I really appreciate I would like to bother you for one last time ( as of now ;). So, if I am dealing with a non-trivial molecule like CNT or some polyelectrolyte and I mainly intend to demonstrate the non-bonding interactions with some nucleic acids (say a CNT-dsDNA ) interaction, it appears to me that I dont need to care about the DNA topology even if it lacks the said parameters but I do have to care about these while updating the cnt.itp files since grompp complains about the missing parameters in the cnt.itp file. If one does not write the [ atomtypes ] and the [ pairtypes ] sections in the cnt.itp file and misses out the sigma and epsilon terms I think it underestimates the non-bonding energy terms of interaction between DNA bases and CNT atoms in the md.edr file to some extent. I will appreciate your opinion on this statement. Thanks for your time in advance Soumadwip Research Fellow IITB India -- 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] regarding pdb2gmx
On 5/31/15 8:37 AM, soumadwip ghosh wrote: Thank you very much for your help Justin. I really appreciate I would like to bother you for one last time ( as of now ;). So, if I am dealing with a non-trivial molecule like CNT or some polyelectrolyte and I mainly intend to demonstrate the non-bonding interactions with some nucleic acids (say a CNT-dsDNA ) interaction, it appears to me that I dont need to care about the DNA topology even if it lacks the said parameters but I do have to care about these while updating the cnt.itp files since grompp complains about the missing parameters in the cnt.itp file. If one does not write the [ atomtypes ] and the [ pairtypes ] sections in the cnt.itp file and misses out the sigma and epsilon terms I think it underestimates the non-bonding energy terms of interaction between DNA bases and CNT atoms in the md.edr file to some extent. I will appreciate your opinion on this statement. That doesn't make sense. If you are missing parameters, grompp will complain and fail with a fatal error. If grompp happily carries on and produces your .tpr, then you're getting the interactions the force field dictates because grompp found everything the molecules need in ffbonded.itp, ffnonbonded.itp, or specified in a molecule .itp. If you override grompp's messages with -maxwarn, well then that's your fault :) Also note that [pairtypes] are intramolecular terms. They do not affect DNA-CNT interactions. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Checksum wrong
That means I can not append to the output file md_0.xvg after rerun free energy simulation? Has anyone experienced this problem before? 2015-05-30 20:42 GMT+02:00 Ahmet Yıldırım ahmedo...@gmail.com: Dear users, When I restart one of lambda points for free energy calculation, Gromacs gives the following error. Whereas the md_0.xvg file exists in the folder. I hope the md_0.xvg can append? Command: mdrun -v -s md_0.tpr -cpi md_0.cpt -cpo md_0-1.cpt -dhdl md_0.xvg -x md_0.xtc -e md_0.edr -g md_0.log -append Fatal error: Checksum wrong for 'md_0.xvg'. The file has been replaced or its contents have been modified. Cannot do appending because of this condition. -- Ahmet Yıldırım -- Ahmet Yıldırım -- 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.
