[gmx-users] GROMACS state-of-the-art setup (was Re: Intermolecular Distance Restraints)
Warren DeLano
warren at delanoscientific.com
Sun Aug 15 19:32:46 CEST 2004
Thanks for the help...pdb2gmx -merge works like a champ.
As far PyMOL goes, I'd like to get a better handle on what the state of the
art is with respect to setting up GROMACS simulations. I'm hoping someone
can answer the following questions:
- Is there currently a way to restrain sub-portions of a system using a
conceptual selection language (ala XPLOR/CNS/PyMOL), rather than atom
identifiers?
For example, in the past I've needed to do stuff like the following.
select ligand, chain A
select protein, chain B
restrain_position (all)
unrestrain_position (ligand)
unrestrain_position (protein within 10 of ligand)
restrain_position (protein///143-144/)
restrain_distance (ligand///5/N), (protein///123/O), 3.2
restrain_distance (ligand///6/O), (protein///122/N), 3.2
in order to set up models where certain interactions or conformations are
assumed/enforced from the get-go.
The above isn't all that far from being doable with PyMOL by using Python to
simple read, edit, and write posre.itp and disre.itp files, but is there
already some other tool which can do this efficiently for GROMACS?
- Is there an easy way to avoid renumbering of residues and chain
identifiers? or a way to correct the final output from GROMACS so that it
matches the naming used in the input PDB?
Setup, analysis, and sharing of results is harder if you're constantly
having to renumber systems, and especially when you're using fixed
identifiers in atom selections as in the above examples. PyMOL could
probably handle the remapping automatically stored the original identifiers
in Python dicts, but perhaps there is already a simple solution to this
problem?
- Is there any GROMACS tool for automatically assigning semi-reasonable
charges and types to arbitrary organic molecules?
I'm not talking about QM-quality parmeterizations, but rather the quick and
dirty (yes, mostly bogus) stuff that industrial computational chemists need
to do on a routine basis in order to rapidly generate crude models of
protein/ligand complexes. PyMOL has a chemical substructure pattern
recognition module that could be useful for this...
Cheers,
Warren
--
mailto:warren at delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of
> gmx-users-request at gromacs.org
> Sent: Sunday, August 15, 2004 3:00 AM
> To: gmx-users at gromacs.org
> Subject: gmx-users Digest, Vol 4, Issue 35
>
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> Today's Topics:
>
> 1. Re: Single precision Compilation error (Tandia, Adama)
> (Pim Schravendijk)
> 2. Re: re:Membrane Peptide+ DPPC+ Water simulation
> (pandey at bioinfo.ernet.in)
> 3. segmentation fault (Dinesh Pinisetty)
> 4. re:Membrane Peptide+ DPPC+ Water simulation (John Simms)
> 5. Re: Intermolecular Distance Restraints (Kay Gottschalk)
> 6. Re:segmentation fault (John Simms)
> 7. Re: segmentation fault (David)
> 8. Re: Intermolecular Distance Restraints (David)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 14 Aug 2004 14:25:43 +0200 (CEST)
> From: Pim Schravendijk <schraven at mpip-mainz.mpg.de>
> Subject: [gmx-users] Re: Single precision Compilation error (Tandia,
> Adama)
> To: gmx-users at gromacs.org
> Message-ID:
> <Pine.LNX.4.58.0408141420060.11451 at pckr37.mpip-mainz.mpg.de>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
>
>
> This seems to be a Tru64 specific problem.
> When looking at:
>
> http://www.google.com/search?q=%22cc:+Fatal:+A+memory+access+v
> iolation%22
>
> I find, amongst others:
>
> http://ftp.support.compaq.com.au/pub/patches/Digital_UNIX/v4.0
> a/DIGITAL_UNIX_V4.0A/doc/txt/OSFPAT00044300405.txt
>
> PROBLEM: (QAR 51448) (Patch ID: OSF405-400187)
> ********
> This patch fixes a crash in the DEC C compiler that occurs
> when compiling a structure whose tag is longer than 256
> characters. The problem occurs only when compiling with
> debug symbols (-g). Below is an example of a program that
> will cause this crash.
> % cat test.c
> #define a(x) x##x##x##x##x##x##x##x##x##x##x##x##x##x##x##x
> struct a(XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX);
> % cc -g test.c
> cc: Fatal: A memory access violation (bus error or
> segmentation fault) has occurred. Please submit a problem report.
>
> Maybe you should try a newer compiler version.
>
> Greetings, Pim
>
> --
> Pim Schravendijk - PhD Student
> Max Planck Institute for Polymer Research
> http://www.mpip-mainz.mpg.de/~schraven/
>
> >
> > Message: 1
> > Date: Fri, 13 Aug 2004 15:56:07 -0400
> > From: "Tandia, Adama" <TandiaA at Corning.com>
> > Subject: [gmx-users] Single precision Compilation error
> > To: "'gmx-users at gromacs.org'" <gmx-users at gromacs.org>
> > Message-ID:
> > <A8976B80EA052A4B8EF816DD3EA0DD0498855F at ROYALOAK.na.corning.com>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > Dear ALL:
> > I was compiling a single precision version 3.2.1 of Gromacs
> and end up with the following error message.
> > Anybody has an idea what is wrong in the setup/compilation/linkage?
> >
> > cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include
> -DGMXLIBDIR=\"/nfs/home/tandia/share/gromacs
> > fs/home/tandia/include -std1 -fast -O4 -no_ifo -arch ev67
> -unroll 2 -fp_reorder -c `test -f 'discecho './'`discopar.c
> > cc: Fatal: A memory access violation (bus error or
> segmentation fault)
> > has occurred. Please submit a problem report.
> > make[3]: *** [discopar.o] Error 1
> >
> > Below are commands for the compilation:
> >
> > export CPPFLAGS=-I/nfs/home/tandia/include
> > export LDFLAGS=-L/nfs/home/tandia/lib
> > ./configure -prefix--$HOME
> > make
> >
> > Adama Tandia
> > Modeling & Simulation
> > Corning INC
> > Corning, NY 14831 USA
> > Tel: 607 248 1036
> > Fax: 607 974 3405
> > www.corning.com <www.corning.com>
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 14 Aug 2004 21:13:54 +0530 (IST)
> From: pandey at bioinfo.ernet.in
> Subject: Re: [gmx-users] re:Membrane Peptide+ DPPC+ Water simulation
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID: <50141.202.41.70.84.1092498234.squirrel at bioinfo.ernet.in>
> Content-Type: text/plain;charset=iso-8859-1
>
>
> Hi all,
>
> Thanks for reply, John.:)
>
> I have used the file provided by you. But, sadly I am still
> getting error.
> The section of error message.
>
> I have followed exactly, what you have said. Renamed the ffG43a2x.itp.
>
> In general I am trying lipid simulation with following step:
>
> 1) Get dppc_npat, dppc.itp and lipid.itp from Prof. Tieleman site.
>
> 2) Get (i)ffG43a2x.tar
> (which has following
> files:ffG43a2x.atp,ffG43a2x-c.tdb,ffG43a2x.itp,ffG43a2x-n.tdb,
> ffG43a2xbon.itp,
> ffG43a2x.hdb, ffG43a2xnb.itp, ffG43a2x.rtp)
> (ii)ffgmx_lipids.tar (which has following files:
> ffgmx.atp, ffgmxbon.itp, ffgmxnb.itp, ffgmx.itp)
>
> (3)use pdb2gmx, editconf, genbox command with appropriate parameter
>
> 4)edit *.top file with following:
> either
> (i)#include ffG43a2x.itp and #include dppc.itp
> or
> (ii)#include ffgmx.itp and #include dppc.itp
> (Note: In both cases i am getting error, which i have mailed
> in group erlier)
> (5)The reason i am not including lipid.itp is two:
> (i) The lipid parameters are already included in the ffgmx.itp and
> ffgmnb.itp (that i got from untaring ffgmx_lipids.tar)
> (ii)When i include, lipid.itp also,the error of "second
> directive comes"
> (6) Get the *.itp file, provided by John, and rename it as
> ffG43a2x.itp.
> (7) Run grompp
> -----------------error while grompp----------
> WARNING 7 [file "dppc.itp", line 229]:
> No default Ryckaert-Bell. types, using zeroes
> WARNING 8 [file "dppc.itp", line 230]:
> No default Ryckaert-Bell. types, using zeroes
> WARNING 9 [file "dppc.itp", line 231]:
> No default Ryckaert-Bell. types, using zeroes
> WARNING 10 [file "dppc.itp", line 232]:
> No default Ryckaert-Bell. types, using zeroes
> Cleaning up temporary file grompppCgmTJ
> Fatal error: Too many warnings, grompp terminated
> ------------------end-----------------
>
> -----------------section of topology file-------
> ; Include forcefield parameters
> #include "ffG43a2x.itp"
> #include "dppc.itp"
> [ moleculetype ]
> ; Name nrexcl
> Protein_A 3
> --------------------end-----------------
>
> Is there any more step to follow, please tell me. I doing
> lipid simulation
> for first time.
>
> Cheers
> Pandey
> -------------
> Research Assistant
> Bioinformatics Center,
> University Of Pune,
> Pune
> India
>
> > Hi,
> > The reason why you are getting the atomtype LC3 error is
> that there is
> > another file on Peter Tielemans web site called lipid.itp
> that you need to
> > include into the non-bonding file which corresponds to the
> forcefield you
> > are using (ie ffG43a2xnb.itp). The dppc.itp file refers to
> parameters
> > within
> > the lipid itself (bond length, angle, charges etc). All
> that you do is cut
> > and paste the corresponding entries from the lipid.itp file into the
> > correct
> > non-bonding file. Another thing is that there is also a
> GROMOS9645a3 also
> > with improved aliphatic hydrocarbon parameters. I havent
> look at this yet,
> > but you may want to.
> > Cheers
> > John
> >
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 14 Aug 2004 15:42:23 -0500
> From: Dinesh Pinisetty <dpinis1 at lsu.edu>
> Subject: [gmx-users] segmentation fault
> To: gmx-users at gromacs.org
> Message-ID:
>
> <OFC5C0EA60.355C8752-ON86256EF0.0071BE97-86256EF0.0071BEB0 at lsu.edu>
> Content-Type: text/plain; charset=US-ASCII
>
>
>
>
>
> Hello everyone,
> when I was trying to do energy minimization of
> DPPC membrane with water I am getting error as
> "SEGMENTATION FAULT".
> I have added water using genbox command,box is
> cubic.
> Could anybody tell me what might be the reason for
> this error...................
> Thank you.
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 14 Aug 2004 23:58:03 +0100
> From: "John Simms" <jxs818 at bham.ac.uk>
> Subject: [gmx-users] re:Membrane Peptide+ DPPC+ Water simulation
> To: <gmx-users at gromacs.org>
> Message-ID: <JIEBKHOPCLKGGBGDJMPNOEGACBAA.jxs818 at bham.ac.uk>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
> Whoops forgot about this bit. All that I did here was to copy the RB
> parameters from ffgmxbon.itp and pasted these values into the
> bon file for
> the forcefield (ie ffG43a2xbon.itp). This is below, so cut
> and paste this at
> the bottom of you ffG43a2xbon.itp file and see how you get
> on. I think this
> was right, but if things go wrong.... ;-). I think that was
> it, but if there
> are more errors just post them up again.
>
> ;from ffG43a2x,itp
> [ dihedraltypes ]
> LP2 LP2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
> LH2 LH2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
> LCH2 LCH2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
>
> Cheers
> John
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Sun, 15 Aug 2004 08:24:20 +0300
> From: Kay Gottschalk <kay.gottschalk at weizmann.ac.il>
> Subject: Re: [gmx-users] Intermolecular Distance Restraints
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <5C3432DC-EE7B-11D8-B6C6-000A9599B076 at weizmann.ac.il>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> It would be great to teach PyMol how to read Gromacs!
> K.
>
> On Aug 13, 2004, at 6:43 AM, Warren DeLano wrote:
>
> > Hello,
> >
> > I've finally learning some GROMACS and have been using it to
> > model/refine
> > some enzyme-substrate complexes. I'd like to be able to build some
> > arbitrary distance constraints into the simulation, but that is
> > starting to
> > look like a problem. Here's the deal:
> >
> > 1) I've got two chains with different termini -- the enzyme
> needs to be
> > NH3+/COO-, but the substrate should be capped ACE/NAC. In order to
> > generate
> > a proper pdb2gmx topology with proper termini, it seems that the
> > enzyme &
> > substrate need to be separate molecules.
> >
> > 2) According to some prior posts on the list, there is no way in
> > GROMACS to
> > define the topology for intermolecular distance restraints.
> >
> > I'm stuck. Is there a general way around this? If not,
> then what's
> > the
> > least painful workaround?
> >
> > Would it be worthwhile teaching PyMOL how to visualize,
> manipulate, &
> > merge
> > GROMACS topologies?
> >
> > Cheers,
> > Warren
> >
> > --
> > mailto:warren at delsci.com
> > Warren L. DeLano, Ph.D.
> > Principal Scientist
> > DeLano Scientific LLC
> > Voice (650)-346-1154
> > Fax (650)-593-4020
> >
> >
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
> Dr. Kay-E. Gottschalk
> Department of Biological Chemistry
> Weizmann Institute of Science
> Rehovot
> Israel
>
>
>
> ------------------------------
>
> Message: 6
> Date: Sun, 15 Aug 2004 10:26:08 +0100
> From: "John Simms" <jxs818 at bham.ac.uk>
> Subject: [gmx-users] Re:segmentation fault
> To: <gmx-users at gromacs.org>
> Message-ID: <JIEBKHOPCLKGGBGDJMPNGEGBCBAA.jxs818 at bham.ac.uk>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi
> i dont know if i can help but do you have any other details about the
> segmentation fault when you EM the dppc bilayer. Is this a
> bilayer you have
> built yourself, have you tried Peter Tieleman for a excellent starting
> structures? If you are adding water with genbox are you getting water
> molecules around the lipid tails?
> Cheers
> John
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Sun, 15 Aug 2004 11:45:25 +0200
> From: David <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] segmentation fault
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1092563125.5096.9.camel at h241n2fls34o1123.telia.com>
> Content-Type: text/plain
>
> On Sat, 2004-08-14 at 22:42, Dinesh Pinisetty wrote:
> >
> >
> > Hello everyone,
> > when I was trying to do energy minimization of
> > DPPC membrane with water I am getting error as
> > "SEGMENTATION FAULT".
> > I have added water using genbox command,box is
> > cubic.
> > Could anybody tell me what might be the reason for
> > this error...................
>
> Could be due to large forces. In fact, almost all SEGV in
> mdrun are due
> to large forces, i.e. non-physical coordinates. This fits
> well with the
> way you built the starting structure.
>
> If you insist on building your own, you might want to start
> with running
> without water, equilibrate and add water after that.
>
> > Thank you.
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> --
> David.
> ______________________________________________________________
> __________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ++++++++++
>
>
>
> ------------------------------
>
> Message: 8
> Date: Sun, 15 Aug 2004 11:49:14 +0200
> From: David <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Intermolecular Distance Restraints
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1092563354.5094.13.camel at h241n2fls34o1123.telia.com>
> Content-Type: text/plain
>
> On Sun, 2004-08-15 at 07:24, Kay Gottschalk wrote:
> > It would be great to teach PyMol how to read Gromacs!
> > K.
> >
> > On Aug 13, 2004, at 6:43 AM, Warren DeLano wrote:
> >
> > > Hello,
> > >
> > > I've finally learning some GROMACS and have been using it to
> > > model/refine
> > > some enzyme-substrate complexes. I'd like to be able to
> build some
> > > arbitrary distance constraints into the simulation, but that is
> > > starting to
> > > look like a problem. Here's the deal:
> > >
> > > 1) I've got two chains with different termini -- the
> enzyme needs to be
> > > NH3+/COO-, but the substrate should be capped ACE/NAC.
> In order to
> > > generate
> > > a proper pdb2gmx topology with proper termini, it seems that the
> > > enzyme &
> > > substrate need to be separate molecules.
> Don't know whether this has been answered before: you need to
> give them
> different chain identifiers, and then pdb2gmx will ask you about the
> termini (maybe you need -ter option)
>
> > >
> > > 2) According to some prior posts on the list, there is no way in
> > > GROMACS to
> > > define the topology for intermolecular distance restraints.
> > >
> Yes, it should work with using pdb2gmx -merge.
>
>
> > > I'm stuck. Is there a general way around this? If not,
> then what's
> > > the
> > > least painful workaround?
> > >
> > > Would it be worthwhile teaching PyMOL how to visualize,
> manipulate, &
> > > merge
> > > GROMACS topologies?
> Definitely...
> --
> David.
> ______________________________________________________________
> __________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ++++++++++
>
>
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
>
>
> End of gmx-users Digest, Vol 4, Issue 35
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