[gmx-users] can you Provide cardiolipin parameter file?
dear sir, I want to do Molecular Dynamics Simulations use gromacs,but I can not find cardiolipins(CL) parameters. can you Provide cardiolipin pdb file and parameter(*itp) file?Which is better united atom force field. thank you very much! -- 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] 回复： can you Provide cardiolipin parameter file?
Shouting, especially after 10 minutes from your first post, will not make people willing to help you. Please be patient and polite. On 9 May 2014 09:14, gejingming 531015...@qq.com wrote: I can not find something I want to ! can you help me? -- 原始邮件 -- 发件人: 我自己的邮箱;531015...@qq.com; 发送时间: 2014年5月9日(星期五) 下午3:01 收件人: gromacs.org_gmx-usersgromacs.org_gmx-users@maillist.sys.kth.se; 主题: [gmx-users] can you Provide cardiolipin parameter file? dear sir, I want to do Molecular Dynamics Simulations use gromacs,but I can not find cardiolipins(CL) parameters. can you Provide cardiolipin pdb file and parameter(*itp) file?Which is better united atom force field. thank you very much! -- 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] 回复： can you Provide cardiolipin parameter file?
thanks a lot for your reply! -- 原始邮件 -- 发件人: 我自己的邮箱;531015...@qq.com; 发送时间: 2014年5月9日(星期五) 下午3:01 收件人: gromacs.org_gmx-usersgromacs.org_gmx-users@maillist.sys.kth.se; 主题: [gmx-users] can you Provide cardiolipin parameter file? dear sir, I want to do Molecular Dynamics Simulations use gromacs,but I can not find cardiolipins(CL) parameters. can you Provide cardiolipin pdb file and parameter(*itp) file?Which is better united atom force field. thank you very much! -- 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] 回复： 回复： can you Provide cardiolipin parameter file?
Cardiolipin (CL), the signature phospholipid of a mitochondrion,has broad mitochondrial activities. The molecular formula:C81H138O17P2. thanks a lot! -- 原始邮件 -- 发件人: Tsjerk Wassenaar;tsje...@gmail.com; 发送时间: 2014年5月9日(星期五) 下午3:37 收件人: Discussion list for GROMACS usersgmx-us...@gromacs.org; 主题: Re: [gmx-users] 回复： can you Provide cardiolipin parameter file? Which cardiolipin? Cheers, Tsjerk On May 9, 2014 9:23 AM, gejingming 531015...@qq.com wrote: thanks a lot for your reply! -- 原始邮件 -- 发件人: 我自己的邮箱;531015...@qq.com; 发送时间: 2014年5月9日(星期五) 下午3:01 收件人: gromacs.org_gmx-usersgromacs.org_gmx-users@maillist.sys.kth.se; 主题: [gmx-users] can you Provide cardiolipin parameter file? dear sir, I want to do Molecular Dynamics Simulations use gromacs,but I can not find cardiolipins(CL) parameters. can you Provide cardiolipin pdb file and parameter(*itp) file?Which is better united atom force field. thank you very much! -- 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] 回复： 回复： can you Provide cardiolipin parameter file?
Hi, Here is a CG one: http://lipidbook.bioch.ox.ac.uk/package/show/id/31.html and here is an atomistic one: http://lipidbook.bioch.ox.ac.uk/package/show/id/61.html The atomistic one was used in a bacterial membrane, so you will likely have to change the tails to make an appropriate mitochondrial lipid. There are likely to be parameters out there for other force fields (for example, I have seen work using both Berger and CHARMM based force fields simulating cardiolipin) so a good search might well find these too. Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of gejingming [531015...@qq.com] Sent: 09 May 2014 09:24 To: 我自己的邮箱 Subject: [gmx-users] 回复： 回复： can you Provide cardiolipin parameter file? Cardiolipin (CL), the signature phospholipid of a mitochondrion,has broad mitochondrial activities. The molecular formula:C81H138O17P2. thanks a lot! -- 原始邮件 -- 发件人: Tsjerk Wassenaar;tsje...@gmail.com; 发送时间: 2014年5月9日(星期五) 下午3:37 收件人: Discussion list for GROMACS usersgmx-us...@gromacs.org; 主题: Re: [gmx-users] 回复： can you Provide cardiolipin parameter file? Which cardiolipin? Cheers, Tsjerk On May 9, 2014 9:23 AM, gejingming 531015...@qq.com wrote: thanks a lot for your reply! -- 原始邮件 -- 发件人: 我自己的邮箱;531015...@qq.com; 发送时间: 2014年5月9日(星期五) 下午3:01 收件人: gromacs.org_gmx-usersgromacs.org_gmx-users@maillist.sys.kth.se; 主题: [gmx-users] can you Provide cardiolipin parameter file? dear sir, I want to do Molecular Dynamics Simulations use gromacs,but I can not find cardiolipins(CL) parameters. can you Provide cardiolipin pdb file and parameter(*itp) file?Which is better united atom force field. thank you very much! -- 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. -- 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 simulation
Dear Justin thanks for your quick reply i,mgoing to simulate zinc ion on Amyloid beta peptide at 300k...and i choose 1ZE9 as pdb my choice is correct or i have to pdb of protein without cation for my work or can i delete zinc ion effect in that pdb? for force field choosing ,i think Opls is appropriate for this simulation...isn,t it? best wishes elham -- 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] Error: dangling bond at atleast one of terminals
Dear users, I am running membrane protein simulation in lipid environment. when I processed through pdb2gmx *pdb2gmx -f 3B5D.pdb -o 3B5D_processed.gro -ignh -ter -water spc* *I get the following out put and error. * *please n* *help* Select the Force Field: From '/opt/bio/gromacs/share/gromacs/top': 1: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (with CMAP) - version 2.0 9: GROMOS96 43a1 force field 10: GROMOS96 43a2 force field (improved alkane dihedrals) 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 15: [DEPRECATED] Encad all-atom force field, using full solvent charges 16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges 17: [DEPRECATED] Gromacs force field (see manual) 18: [DEPRECATED] Gromacs force field with hydrogens for NMR 13 Using the Gromos53a6 force field in directory gromos53a6.ff Opening force field file /opt/bio/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading 3B5D.pdb... WARNING: all CONECT records are ignored Read 'MULTIDRUG TRANSPORTER EMRE; 5 VIOLOGEN RESISTANCE PROTEIN C, ETHIDIUM RESISTANCE PROTEIN', 224 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. WARNING: Chain identifier 'A' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. There are 3 chains and 0 blocks of water and 350 residues with 224 atoms chain #res #atoms 1 'A' 100100 2 'B'99 99 3 'A' 1 25 All occupancies are one Opening force field file /opt/bio/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (gromos53a6) Opening force field file /opt/bio/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 108 Sorting it all out... Opening force field file /opt/bio/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb Opening force field file /opt/bio/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file /opt/bio/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.4# Processing chain 1 'A' (100 atoms, 100 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Identified residue TYR6 as a starting terminus. Identified residue SER105 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for TYR-6 0: NH3+ 1: NH2 2: None 2 Start terminus TYR-6: None Select end terminus type for SER-105 0: COO- 1: COOH 2: None 2 End terminus SER-105: None --- Program pdb2gmx, VERSION 4.5.4 Source code file: pdb2top.c, line: 1035 F*atal error:* *There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.* *For more information and tips for troubleshooting, please check the GROMACS* *website at http://www.gromacs.org/Documentation/Errors http://www.gromacs.org/Documentation/Errors* regards -- B.Suriyanarayanan -- 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] Force Field for Bilayer Simulations with Cholesterol and Proteins
Hi, I used ffgmx.itp. It contains CB. BR, Samuli Ollila From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of David Ackerman [da...@cornell.edu] Sent: Wednesday, May 07, 2014 10:30 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Force Field for Bilayer Simulations with Cholesterol and Proteins Thank you for your advice. Which force field was used? I have downloaded the cholesterol parameters from Höltje et al, but atomtypes like CB do not exist in the force field I am using (53a6). Did you change these to other atomtypes as well, or were you using a force field that included them? -David On Wed, May 7, 2014 at 8:59 AM, Ollila Samuli samuli.oll...@aalto.fiwrote: Hi, In my understanding the CH2-LP2 attraction is stronger than LP2-LP2 attraction in the Berger/Höltje combination you described. If you then have CH2 groups in cholesterol and LP2 groups in lipids, it might lead to too condensed bilayer. I think that the related issue is discussed here: http://dx.doi.org/10.1088/0953-8984/18/28/S07 and here: http://dx.doi.org/10.1039/C2CP42738A we have changed the CH2 groups in cholesterol to LP2 groups and compared the results quite extensively to the NMR measurements. BR, Samuli Ollila From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of David Ackerman [da...@cornell.edu] Sent: Monday, May 05, 2014 7:39 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Force Field for Bilayer Simulations with Cholesterol and Proteins Hello, I have been performing simulations of multi-component bilayers using parameters described in the following paper: http://www.ncbi.nlm.nih.gov/pubmed/23470157. They use the ffgmx forcefield with Berger lipid parameters included. They also use cholesterol from Holtje et. al ( http://www.sciencedirect.com/science/article/pii/S000527360100270X), which was parameterized for the ffgmx force field. I noticed that unlike the KALP-15 GROMACS tutorial which suggests deleting the default lipid-gromos Berger interactions, the authors kept those interactions in the force field. In light of newer force fields, are these older force fields wither Berger parameters still acceptable? The cholesterol model seems commonly used, so I am unsure how to use cholesterol with a newer force field. Furthermore, if I were to include proteins in the simulation, would I still be able to use the same ffgmx force field with Berger parameters (including lipid-gromos interactions)? Thank you, David -- 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.
[gmx-users] 回复： 回复： 回复： can you Provide cardiolipin parameter file?
thank you very much for your reply! -- 原始邮件 -- 发件人: Piggot T.;t.pig...@soton.ac.uk; 发送时间: 2014年5月9日(星期五) 下午5:23 收件人: gmx-us...@gromacs.orggmx-us...@gromacs.org; 主题: Re: [gmx-users] 回复： 回复： can you Provide cardiolipin parameter file? Hi, Here is a CG one: http://lipidbook.bioch.ox.ac.uk/package/show/id/31.html and here is an atomistic one: http://lipidbook.bioch.ox.ac.uk/package/show/id/61.html The atomistic one was used in a bacterial membrane, so you will likely have to change the tails to make an appropriate mitochondrial lipid. There are likely to be parameters out there for other force fields (for example, I have seen work using both Berger and CHARMM based force fields simulating cardiolipin) so a good search might well find these too. Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of gejingming [531015...@qq.com] Sent: 09 May 2014 09:24 To: 我自己的邮箱 Subject: [gmx-users] 回复： 回复： can you Provide cardiolipin parameter file? Cardiolipin (CL), the signature phospholipid of a mitochondrion,has broad mitochondrial activities. The molecular formula:C81H138O17P2. thanks a lot! -- 原始邮件 -- 发件人: Tsjerk Wassenaar;tsje...@gmail.com; 发送时间: 2014年5月9日(星期五) 下午3:37 收件人: Discussion list for GROMACS usersgmx-us...@gromacs.org; 主题: Re: [gmx-users] 回复： can you Provide cardiolipin parameter file? Which cardiolipin? Cheers, Tsjerk On May 9, 2014 9:23 AM, gejingming 531015...@qq.com wrote: thanks a lot for your reply! -- 原始邮件 -- 发件人: 我自己的邮箱;531015...@qq.com; 发送时间: 2014年5月9日(星期五) 下午3:01 收件人: gromacs.org_gmx-usersgromacs.org_gmx-users@maillist.sys.kth.se; 主题: [gmx-users] can you Provide cardiolipin parameter file? dear sir, I want to do Molecular Dynamics Simulations use gromacs,but I can not find cardiolipins(CL) parameters. can you Provide cardiolipin pdb file and parameter(*itp) file?Which is better united atom force field. thank you very much! -- 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. -- 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] Force Field for Bilayer Simulations with Cholesterol and Proteins
Hi David, Firstly I would say, is there any reason why you need to use the Berger/Höltje/GROMOS force field combination? There are several other options available that I can think of which may be easier/better for you. You could use the Slipids (with an AMBER force field for the protein), CHARMM36 for all of the components of your system, or if you do want to stick with a united-atom force field, you could still use one of the GROMOS force fields ((e.g. 54A7) with the GROMOS-CKP lipids and the consistent cholesterol parameters that you can download from the manual entry of the automated topology builder. I haven't ever simulated cholesterol so I cannot really recommend which may be better than others for this molecule, but there will be plenty of literature out there to look at regarding this. Secondly, if you do want to stay with the Berger/Höltje/GROMOS combination, you could probably add the missing atomtypes to the GROMOS force field you wish to use. I would strongly advise against using the old 'ffgmx' force field, this has been shown to behave pretty poorly for proteins. Do be careful in doing this addition of atomtypes, as the GROMOS force fields are different from the all-atom force fields in as much as the atomtypes have multiple van der Waals interaction parameters used for interactions with different atomtypes. Some of the GROMOS papers describe this in far more detail. Just some of my thoughts, hopefully of some use! Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Ollila Samuli [samuli.oll...@aalto.fi] Sent: 09 May 2014 11:42 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force Field for Bilayer Simulations with Cholesterol and Proteins Hi, I used ffgmx.itp. It contains CB. BR, Samuli Ollila From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of David Ackerman [da...@cornell.edu] Sent: Wednesday, May 07, 2014 10:30 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Force Field for Bilayer Simulations with Cholesterol and Proteins Thank you for your advice. Which force field was used? I have downloaded the cholesterol parameters from Höltje et al, but atomtypes like CB do not exist in the force field I am using (53a6). Did you change these to other atomtypes as well, or were you using a force field that included them? -David On Wed, May 7, 2014 at 8:59 AM, Ollila Samuli samuli.oll...@aalto.fiwrote: Hi, In my understanding the CH2-LP2 attraction is stronger than LP2-LP2 attraction in the Berger/Höltje combination you described. If you then have CH2 groups in cholesterol and LP2 groups in lipids, it might lead to too condensed bilayer. I think that the related issue is discussed here: http://dx.doi.org/10.1088/0953-8984/18/28/S07 and here: http://dx.doi.org/10.1039/C2CP42738A we have changed the CH2 groups in cholesterol to LP2 groups and compared the results quite extensively to the NMR measurements. BR, Samuli Ollila From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of David Ackerman [da...@cornell.edu] Sent: Monday, May 05, 2014 7:39 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Force Field for Bilayer Simulations with Cholesterol and Proteins Hello, I have been performing simulations of multi-component bilayers using parameters described in the following paper: http://www.ncbi.nlm.nih.gov/pubmed/23470157. They use the ffgmx forcefield with Berger lipid parameters included. They also use cholesterol from Holtje et. al ( http://www.sciencedirect.com/science/article/pii/S000527360100270X), which was parameterized for the ffgmx force field. I noticed that unlike the KALP-15 GROMACS tutorial which suggests deleting the default lipid-gromos Berger interactions, the authors kept those interactions in the force field. In light of newer force fields, are these older force fields wither Berger parameters still acceptable? The cholesterol model seems commonly used, so I am unsure how to use cholesterol with a newer force field. Furthermore, if I were to include proteins in the simulation, would I still be able to use the same ffgmx force field with Berger parameters (including lipid-gromos interactions)? Thank you, David -- 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] Force Field for Bilayer Simulations with Cholesterol and Proteins
On 2014-05-09 13:47, Piggot T. wrote: Hi David, Firstly I would say, is there any reason why you need to use the Berger/Höltje/GROMOS force field combination? There are several other options available that I can think of which may be easier/better for you. You could use the Slipids (with an AMBER force field for the protein), CHARMM36 for all of the components of your system, or if you do want to stick with a united-atom force field, you could still use one of the GROMOS force fields ((e.g. 54A7) with the GROMOS-CKP lipids and the consistent cholesterol parameters that you can download from the manual entry of the automated topology builder. I haven't ever simulated cholesterol so I cannot really recommend which may be better than others for this molecule, but there will be plenty of literature out there to look at regarding this. Secondly, if you do want to stay with the Berger/Höltje/GROMOS combination, you could probably add the missing atomtypes to the GROMOS force field you wish to use. I would strongly advise against using the old 'ffgmx' force field, this has been shown to behave pretty poorly for proteins. Do be careful in doing this addition of atomtypes, as the GROMOS force fields are different from the all-atom force fields in as much as the atomtypes have multiple van der Waals interaction parameters used for interactions with different atomtypes. Some of the GROMOS papers describe this in far more detail. Just some of my thoughts, hopefully of some use! You could also look here: http://cmb.bio.uni-goettingen.de/downloads.html Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Ollila Samuli [samuli.oll...@aalto.fi] Sent: 09 May 2014 11:42 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force Field for Bilayer Simulations with Cholesterol and Proteins Hi, I used ffgmx.itp. It contains CB. BR, Samuli Ollila From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of David Ackerman [da...@cornell.edu] Sent: Wednesday, May 07, 2014 10:30 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Force Field for Bilayer Simulations with Cholesterol and Proteins Thank you for your advice. Which force field was used? I have downloaded the cholesterol parameters from Höltje et al, but atomtypes like CB do not exist in the force field I am using (53a6). Did you change these to other atomtypes as well, or were you using a force field that included them? -David On Wed, May 7, 2014 at 8:59 AM, Ollila Samuli samuli.oll...@aalto.fiwrote: Hi, In my understanding the CH2-LP2 attraction is stronger than LP2-LP2 attraction in the Berger/Höltje combination you described. If you then have CH2 groups in cholesterol and LP2 groups in lipids, it might lead to too condensed bilayer. I think that the related issue is discussed here: http://dx.doi.org/10.1088/0953-8984/18/28/S07 and here: http://dx.doi.org/10.1039/C2CP42738A we have changed the CH2 groups in cholesterol to LP2 groups and compared the results quite extensively to the NMR measurements. BR, Samuli Ollila From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of David Ackerman [da...@cornell.edu] Sent: Monday, May 05, 2014 7:39 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Force Field for Bilayer Simulations with Cholesterol and Proteins Hello, I have been performing simulations of multi-component bilayers using parameters described in the following paper: http://www.ncbi.nlm.nih.gov/pubmed/23470157. They use the ffgmx forcefield with Berger lipid parameters included. They also use cholesterol from Holtje et. al ( http://www.sciencedirect.com/science/article/pii/S000527360100270X), which was parameterized for the ffgmx force field. I noticed that unlike the KALP-15 GROMACS tutorial which suggests deleting the default lipid-gromos Berger interactions, the authors kept those interactions in the force field. In light of newer force fields, are these older force fields wither Berger parameters still acceptable? The cholesterol model seems commonly used, so I am unsure how to use cholesterol with a newer force field. Furthermore, if I were to include proteins in the simulation, would I still be able to use the same ffgmx force field with Berger parameters (including lipid-gromos interactions)? Thank you, David -- 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
Re: [gmx-users] Error: dangling bond at atleast one of terminals
On 5/9/14, 6:25 AM, Balasubramanian Suriyanarayanan wrote: Dear users, I am running membrane protein simulation in lipid environment. when I processed through pdb2gmx *pdb2gmx -f 3B5D.pdb -o 3B5D_processed.gro -ignh -ter -water spc* *I get the following out put and error. * *please n* *help* Select the Force Field: From '/opt/bio/gromacs/share/gromacs/top': 1: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (with CMAP) - version 2.0 9: GROMOS96 43a1 force field 10: GROMOS96 43a2 force field (improved alkane dihedrals) 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 15: [DEPRECATED] Encad all-atom force field, using full solvent charges 16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges 17: [DEPRECATED] Gromacs force field (see manual) 18: [DEPRECATED] Gromacs force field with hydrogens for NMR 13 Using the Gromos53a6 force field in directory gromos53a6.ff Opening force field file /opt/bio/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading 3B5D.pdb... WARNING: all CONECT records are ignored Read 'MULTIDRUG TRANSPORTER EMRE; 5 VIOLOGEN RESISTANCE PROTEIN C, ETHIDIUM RESISTANCE PROTEIN', 224 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. WARNING: Chain identifier 'A' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. There are 3 chains and 0 blocks of water and 350 residues with 224 atoms chain #res #atoms 1 'A' 100100 2 'B'99 99 3 'A' 1 25 All occupancies are one Opening force field file /opt/bio/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (gromos53a6) Opening force field file /opt/bio/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 108 Sorting it all out... Opening force field file /opt/bio/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb Opening force field file /opt/bio/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file /opt/bio/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.4# Processing chain 1 'A' (100 atoms, 100 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Identified residue TYR6 as a starting terminus. Identified residue SER105 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for TYR-6 0: NH3+ 1: NH2 2: None 2 Start terminus TYR-6: None Select end terminus type for SER-105 0: COO- 1: COOH 2: None 2 End terminus SER-105: None --- Program pdb2gmx, VERSION 4.5.4 Source code file: pdb2top.c, line: 1035 F*atal error:* *There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.* *For more information and tips for troubleshooting, please check the GROMACS* *website at http://www.gromacs.org/Documentation/Errors http://www.gromacs.org/Documentation/Errors* Choosing None for your termini doesn't make sense. You will have incomplete amide groups. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] force field
On 5/9/14, 1:12 AM, elham tazikeh wrote: Dear Justin thanks for your quick reply i,mgoing to simulate zinc ion on Amyloid beta peptide at 300k...and i choose 1ZE9 as pdb my choice is correct or i have to pdb of protein without cation for my work or can i delete zinc ion effect in that pdb? for force field choosing ,i think Opls is appropriate for this simulation...isn,t it? These are all issues you should discuss with an adviser and colleagues. If you have Gromacs-specific questions, post them here, but the purpose of this list is not to design your experiments for you. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] energy
On 5/9/14, 6:28 AM, mirko busato wrote: Dear Users, In my experiment, one petide of troponin protein and many copies of the same type of monomer, itaconic acid,(negatively charged) are assembled in a virtual box. I would like to understand , if there is a method to calculate the interaction energy between the peptide and the monomers. That's what energygrps are for. -Justin I am asking this because I would like to have an energetic value to determine the affinity of the itaconic acid monomer against the peptide. My system is in vacuum and NA sodium ions weren't added to neutralize the system, so my system is charged. The force field used is CHARMM27 and I performed a minimization energy step and an equilibration step. Could you help me? Thank you very much, Mirko -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] energy
Dear Justin, Thank you very much for your quick reply, In my .mdp file I set up energygrps to protein ITA. (ITA is the group for the Itaconic acid monomers) After that I tried to launch g_energy command on .edr file. Is it right? which energy terms do you suggest me to use for my problem (to understand the affinity peptide-monomer)? Thank you very much, Mirko On Friday, May 9, 2014 2:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/9/14, 6:28 AM, mirko busato wrote: Dear Users, In my experiment, one petide of troponin protein and many copies of the same type of monomer, itaconic acid,(negatively charged) are assembled in a virtual box. I would like to understand , if there is a method to calculate the interaction energy between the peptide and the monomers. That's what energygrps are for. -Justin I am asking this because I would like to have an energetic value to determine the affinity of the itaconic acid monomer against the peptide. My system is in vacuum and NA sodium ions weren't added to neutralize the system, so my system is charged. The force field used is CHARMM27 and I performed a minimization energy step and an equilibration step. Could you help me? Thank you very much, Mirko -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] Can't make links on GROMACS
I mean that it is a bug because you can't make link after build from the source, although it is easy to work around with it. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] MD simulation at pH 2
Hi all, I have the 8-residue peptide and I want to do Molecular Dynamics simulations at pH 2 (with explicit solvent). To do this, I added three Hydrogen atoms to two of the 8-residue peptite (one Hydrogen to the Glu, two Hydrojen to the Asp). And also I choose the NH3 for the start terminus and COOH for the end terminus. Finally, I get the my peptide at pH 2. And than, I plan to follow the usual procedure (define box, fill the box with water, energy minim, md...) But, still I am not sure whether this way is correct to get simulation at pH 2 or not? Because when I look at the XXX.gro file (and also topol.top) after the pdb2gmx –f XXX.pdb, I couldn’t see the new-added hydrogens. If you could help me, I would be very happy. with my best regards, Turgay -- 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] MD simulation at pH 2
Nice to know that acidic pH simulations are that easy. Why do you conclude that you achieved pH 2? Dr. Vitaly V. Chaban On Fri, May 9, 2014 at 3:45 PM, Turgay Cakmak turgaycakma...@gmail.com wrote: Hi all, I have the 8-residue peptide and I want to do Molecular Dynamics simulations at pH 2 (with explicit solvent). To do this, I added three Hydrogen atoms to two of the 8-residue peptite (one Hydrogen to the Glu, two Hydrojen to the Asp). And also I choose the NH3 for the start terminus and COOH for the end terminus. Finally, I get the my peptide at pH 2. And than, I plan to follow the usual procedure (define box, fill the box with water, energy minim, md...) But, still I am not sure whether this way is correct to get simulation at pH 2 or not? Because when I look at the XXX.gro file (and also topol.top) after the pdb2gmx –f XXX.pdb, I couldn’t see the new-added hydrogens. If you could help me, I would be very happy. with my best regards, Turgay -- 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] Force Field for Bilayer Simulations with Cholesterol and Proteins
Hello, I appreciate all the responses. I would like to keep my simulations United Atom. And the paper I am basing my work and parameter files on used ffgmx with the Holtje cholesterol and Berger parameters for the lipids. Therefore, most of the interactions are Berger interactions, except for the Berger-Gromos interactions of lipid to cholesterol. I now have learned that a modified cholesterol with Berger parameters might be better and would reduce effects of overcondensation. I plan on testing 53a6 with Berger lipid parameters and modified cholesterol (with Berger LP2 and LP3 replacing CH2 and CH3) to see if it has any significant qualitative effects on my results for a protein-free bilayer. This would be especially important if I want to compare these results with a protein-containing bilayer, since I've come to realize the gmx force field is not the best for proteins. -David On Fri, May 9, 2014 at 8:02 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2014-05-09 13:47, Piggot T. wrote: Hi David, Firstly I would say, is there any reason why you need to use the Berger/Höltje/GROMOS force field combination? There are several other options available that I can think of which may be easier/better for you. You could use the Slipids (with an AMBER force field for the protein), CHARMM36 for all of the components of your system, or if you do want to stick with a united-atom force field, you could still use one of the GROMOS force fields ((e.g. 54A7) with the GROMOS-CKP lipids and the consistent cholesterol parameters that you can download from the manual entry of the automated topology builder. I haven't ever simulated cholesterol so I cannot really recommend which may be better than others for this molecule, but there will be plenty of literature out there to look at regarding this. Secondly, if you do want to stay with the Berger/Höltje/GROMOS combination, you could probably add the missing atomtypes to the GROMOS force field you wish to use. I would strongly advise against using the old 'ffgmx' force field, this has been shown to behave pretty poorly for proteins. Do be careful in doing this addition of atomtypes, as the GROMOS force fields are different from the all-atom force fields in as much as the atomtypes have multiple van der Waals interaction parameters used for interactions with different atomtypes. Some of the GROMOS papers describe this in far more detail. Just some of my thoughts, hopefully of some use! You could also look here: http://cmb.bio.uni-goettingen.de/downloads.html Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Ollila Samuli [samuli.oll...@aalto.fi] Sent: 09 May 2014 11:42 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force Field for Bilayer Simulations with Cholesterol and Proteins Hi, I used ffgmx.itp. It contains CB. BR, Samuli Ollila From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of David Ackerman [da...@cornell.edu] Sent: Wednesday, May 07, 2014 10:30 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Force Field for Bilayer Simulations with Cholesterol and Proteins Thank you for your advice. Which force field was used? I have downloaded the cholesterol parameters from Höltje et al, but atomtypes like CB do not exist in the force field I am using (53a6). Did you change these to other atomtypes as well, or were you using a force field that included them? -David On Wed, May 7, 2014 at 8:59 AM, Ollila Samuli samuli.oll...@aalto.fi wrote: Hi, In my understanding the CH2-LP2 attraction is stronger than LP2-LP2 attraction in the Berger/Höltje combination you described. If you then have CH2 groups in cholesterol and LP2 groups in lipids, it might lead to too condensed bilayer. I think that the related issue is discussed here: http://dx.doi.org/10.1088/0953-8984/18/28/S07 and here: http://dx.doi.org/10.1039/C2CP42738A we have changed the CH2 groups in cholesterol to LP2 groups and compared the results quite extensively to the NMR measurements. BR, Samuli Ollila From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of David Ackerman [da...@cornell.edu] Sent: Monday, May 05, 2014 7:39 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Force Field for Bilayer Simulations with Cholesterol and Proteins Hello, I have been performing simulations of multi-component bilayers using parameters described in the following paper: http://www.ncbi.nlm.nih.gov/pubmed/23470157. They use the ffgmx forcefield with Berger lipid parameters
Re: [gmx-users] MD simulation at pH 2
On 5/9/14, 9:45 AM, Turgay Cakmak wrote: Hi all, I have the 8-residue peptide and I want to do Molecular Dynamics simulations at pH 2 (with explicit solvent). To do this, I added three Hydrogen atoms to two of the 8-residue peptite (one Hydrogen to the Glu, two Hydrojen to the Asp). And also I choose the NH3 for the start terminus and COOH for the end terminus. Finally, I get the my peptide at pH 2. And than, I plan to follow the usual procedure (define box, fill the box with water, energy minim, md...) But, still I am not sure whether this way is correct to get simulation at pH 2 or not? Because when I look at the XXX.gro file (and also topol.top) after the pdb2gmx –f XXX.pdb, I couldn’t see the new-added hydrogens. No, that's not a simulation at pH 2, but it is a simulation of the predominant form of the peptide at pH 2. The missing piece of the puzzle here is what your actual pdb2gmx command was. If you didn't tell pdb2gmx to protonate Glu and Asp (using -glu and -asp, respectively), then it will default to the normal deprotonated forms. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] energy
On 5/9/14, 9:38 AM, mirko busato wrote: Dear Justin, Thank you very much for your quick reply, In my .mdp file I set up energygrps to protein ITA. (ITA is the group for the Itaconic acid monomers) After that I tried to launch g_energy command on .edr file. Is it right? which energy terms do you suggest me to use for my problem (to understand the affinity peptide-monomer)? The short-range nonbonded terms are the only ones that get decomposed in a pairwise fashion, so the new terms should be fairly obvious from the screen output. Whether or not those numbers mean anything is another story; they may give you some insight into the enthalpic driving forces, but they tell you nothing of the actual free energy of binding. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] Can't make links on GROMACS
On 5/9/14, 8:41 AM, Ooker wrote: I mean that it is a bug because you can't make link after build from the source, although it is easy to work around with it. It's not a bug, it looks like the build target for making links has simply been removed, likely a consequence of the complete restructuring of the code and executables themselves. Sourcing GMXRC is the most straightforward way to configure your environment to use Gromacs. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] Can't make links on GROMACS
On Fri, May 9, 2014 at 6:11 PM, Ooker ganuongp...@gmail.com wrote: I mean that it is a bug because you can't make link after build from the source, although it is easy to work around with it. If you are not the super user, you cannot make links. -- 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. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune 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.
[gmx-users] vdw radii in g_sas
Hi All, In the local copy of vdwradii.dat for g_sas calculations, the vdw radii are very approximate. Eg. C = 0.15 nm in vdwradii.dat, whereas ffnonbonded says sigma = 0.367 nm = vdwradius=0.185 nm Is it prudent to replace the values in the local vdwradii.dat with the vdwradii derived from ffnonbonded values? I would love to hear your thoughts/suggestions. Thanks, -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] vdw radii in g_sas
On 5/9/14, 12:23 PM, rajat desikan wrote: Hi All, In the local copy of vdwradii.dat for g_sas calculations, the vdw radii are very approximate. Eg. C = 0.15 nm in vdwradii.dat, whereas ffnonbonded says sigma = 0.367 nm = vdwradius=0.185 nm Is it prudent to replace the values in the local vdwradii.dat with the vdwradii derived from ffnonbonded values? I would love to hear your thoughts/suggestions. No. The value of sigma will not give you the van der Waals radius of an atom. For each force field, the value is different, and it is based on optimized intermolecular distances. I don't think there's a clear way to turn this into some measure of an atom's size. If you're concerned that the values in vdwradii.dat are not sufficiently accurate, replace them with real experimentally determined values. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
[gmx-users] Truncated .trr file size - 20% smaller than expected
Hi there this is my first time posting here so my apologies if I disregard any general formatting rules! In any event on to my question/problem. I am fairly new to MD simulations with much more background on the biological side than the simulation side. That being said, I have been receiving training from another member in the lab and have just started my simulations of a 325 residue protein using GROMACS 4.5.5. My issue has come from the fact that when I grompp my EM.mdp, NVT.mdp, or MPT.mdp files everything seems to be fine ie. No errors or issues and the file sizes match the expected output size. However, when I run my simulation I'm getting about a %20 decrease in the size of my .trr file from what it expects. From my .out file for the molecular dynamics run I get 'WARNING: This run will generate roughly 24940 Mb of data' Actual amount of data produced is ~18 Gb of data. There are no errors running gmx_check on any of the tpr files are anything else I've tried running the same simulation on two different supercomputing clusters to see if the same error occurs just in case it was an issue of the build version having any effect on the size and run into the same problems I've tried running the simulation in parts just in case there was some memory issue causing some problem that I wasn't aware of or looking for I've gotten my labmate and one more person familiar with GROMACS to look at my issued commands and they seem stumped I've also tried running it on 4.6.3 with the verlet cutoff scheme as I was having some issues with pp/pme load balance Nothing so far has made a difference and although the data seems to be fine I'm loathe to do all the analysis if there is something majorly wrong with my simulation. Problem for me is I don't know if or by how much the actual trr file size should change from the expected amounts. Command submitted: mdrun_mpi -npme -1 -s MD.tpr -o MD.trr -x MD.xtc -c MD.pdb -e MD.edr -g MD.log -v -dlb yes -cpo MD.cpt I am running/wanting to run my simulations for 25 - 50ns Thanks in advance for any help and all the best! -Doug --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Truncated .trr file size - 20% smaller than expected
On 5/9/14, 1:46 PM, Douglas Grahame wrote: Hi there this is my first time posting here so my apologies if I disregard any general formatting rules! In any event on to my question/problem. I am fairly new to MD simulations with much more background on the biological side than the simulation side. That being said, I have been receiving training from another member in the lab and have just started my simulations of a 325 residue protein using GROMACS 4.5.5. My issue has come from the fact that when I grompp my EM.mdp, NVT.mdp, or MPT.mdp files everything seems to be fine ie. No errors or issues and the file sizes match the expected output size. However, when I run my simulation I'm getting about a %20 decrease in the size of my .trr file from what it expects. From my .out file for the molecular dynamics run I get 'WARNING: This run will generate roughly 24940 Mb of data' Actual amount of data produced is ~18 Gb of data. There are no errors running gmx_check on any of the tpr files are anything else I've tried running the same simulation on two different supercomputing clusters to see if the same error occurs just in case it was an issue of the build version having any effect on the size and run into the same problems I've tried running the simulation in parts just in case there was some memory issue causing some problem that I wasn't aware of or looking for I've gotten my labmate and one more person familiar with GROMACS to look at my issued commands and they seem stumped I've also tried running it on 4.6.3 with the verlet cutoff scheme as I was having some issues with pp/pme load balance Nothing so far has made a difference and although the data seems to be fine I'm loathe to do all the analysis if there is something majorly wrong with my simulation. Problem for me is I don't know if or by how much the actual trr file size should change from the expected amounts. Command submitted: mdrun_mpi -npme -1 -s MD.tpr -o MD.trr -x MD.xtc -c MD.pdb -e MD.edr -g MD.log -v -dlb yes -cpo MD.cpt For what it's worth, save yourself some typing with: mdrun_mpi -npme -1 -deffnm MD -dlb yes I am running/wanting to run my simulations for 25 - 50ns Probably the grompp estimate is just off. If gmxcheck confirms you have everything you should, there's no reason to think there is a problem. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] vdw radii in g_sas
On 5/9/14, 3:35 PM, rajat desikan wrote: Thanks Justin. I am curious about the value for a phosphorus atom (protein in phospholipid bilayer; g_sas issues a warning). Do you know any reference for experimental values? Google knows. -Justin On Friday, May 9, 2014, Justin Lemkul jalem...@vt.edu wrote: On 5/9/14, 12:23 PM, rajat desikan wrote: Hi All, In the local copy of vdwradii.dat for g_sas calculations, the vdw radii are very approximate. Eg. C = 0.15 nm in vdwradii.dat, whereas ffnonbonded says sigma = 0.367 nm = vdwradius=0.185 nm Is it prudent to replace the values in the local vdwradii.dat with the vdwradii derived from ffnonbonded values? I would love to hear your thoughts/suggestions. No. The value of sigma will not give you the van der Waals radius of an atom. For each force field, the value is different, and it is based on optimized intermolecular distances. I don't think there's a clear way to turn this into some measure of an atom's size. If you're concerned that the values in vdwradii.dat are not sufficiently accurate, replace them with real experimentally determined values. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] vdw radii in g_sas
Do mind that the radius for P in PO4 is different from that for P alone. Cheers, Tsjerk On May 9, 2014 10:53 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/9/14, 3:35 PM, rajat desikan wrote: Thanks Justin. I am curious about the value for a phosphorus atom (protein in phospholipid bilayer; g_sas issues a warning). Do you know any reference for experimental values? Google knows. -Justin On Friday, May 9, 2014, Justin Lemkul jalem...@vt.edu wrote: On 5/9/14, 12:23 PM, rajat desikan wrote: Hi All, In the local copy of vdwradii.dat for g_sas calculations, the vdw radii are very approximate. Eg. C = 0.15 nm in vdwradii.dat, whereas ffnonbonded says sigma = 0.367 nm = vdwradius=0.185 nm Is it prudent to replace the values in the local vdwradii.dat with the vdwradii derived from ffnonbonded values? I would love to hear your thoughts/suggestions. No. The value of sigma will not give you the van der Waals radius of an atom. For each force field, the value is different, and it is based on optimized intermolecular distances. I don't think there's a clear way to turn this into some measure of an atom's size. If you're concerned that the values in vdwradii.dat are not sufficiently accurate, replace them with real experimentally determined values. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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. -- 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] gen pairs missing from vmd top
Hi All I am using topo writegmxtop output.top in VMD and it writes fake sort of top file which needs further user based adjustments. The top file so generated has all [bonds] [angles] [dihedral] information but [pairs] are missing. I am using charmm36 which says gen-pair =yes in forcefield.itp. Does this mean it won't matter if I include or not [pairs] information in top file? pdb2gmx does explicitly prints [pairs] information when I generate top file for some default residues in rtp file. So should I mention them explicitly? Is there any script/command which can generate them as I have bond information (one can write own script simply if its a linear molecule but branching makes thing difficult). thanks JIom -- 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] gen pairs missing from vmd top
On 5/9/14, 7:35 PM, gromacs query wrote: Hi All I am using topo writegmxtop output.top in VMD and it writes fake sort of top file which needs further user based adjustments. The top file so generated has all [bonds] [angles] [dihedral] information but [pairs] are missing. I am using charmm36 which says gen-pair =yes in forcefield.itp. Does this mean it won't matter if I include or not [pairs] information in top file? pdb2gmx does explicitly prints [pairs] information when I generate top file for some default residues in rtp file. So should I mention them explicitly? Is there any script/command which can generate them as I have bond information (one can write own script simply if its a linear molecule but branching makes thing difficult). Pairs do need to be listed explicitly in the .top file. The gen-pairs keyword only affects the generation of pairtypes; if set to yes it will use normal combination rules for any pair that does not have [pairtypes] explicitly listed in ffbonded.itp (which, in the case of CHARMM, is all of them). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
