[gmx-users] gromacs.org_gmx-users Digest, Vol 133, Issue 107
sunita gupta
sunita.bio at gmail.com
Wed May 20 15:54:41 CEST 2015
Thanks Justin for your reply
Below is the file where I added h1 parameters in gbsa.itp...In the same
way I added the parameters for all the possible atomtypes from gaff ff
[ implicit_genborn_params ]
; atype sar st pi gbr hct
;Br 0.1 1 1 0.125 0.85 ; H
C 0.172 1 1.554 0.1875 0.72 ; C
CA 0.18 1 1.037 0.1875 0.72 ; C
CB 0.172 0.012 1.554 0.1875 0.72 ; C
CC 0.172 1 1.554 0.1875 0.72 ; C
CN 0.172 0.012 1.554 0.1875 0.72 ; C
CR 0.18 1 1.073 0.1875 0.72 ; C
CT 0.18 1 1.276 0.190 0.72 ; C
CV 0.18 1 1.073 0.1875 0.72 ; C
CW 0.18 1 1.073 0.1875 0.72 ; C
C* 0.172 0.012 1.554 0.1875 0.72 ; C
H 0.1 1 1 0.115 0.85 ; H
HC 0.1 1 1 0.125 0.85 ; H
H1 0.1 1 1 0.125 0.85 ; H
HA 0.1 1 1 0.125 0.85 ; H
H4 0.1 1 1 0.115 0.85 ; H
H5 0.1 1 1 0.125 0.85 ; H
HO 0.1 1 1 0.105 0.85 ; H
HS 0.1 1 1 0.125 0.85 ; H
HP 0.1 1 1 0.125 0.85 ; H
N 0.155 1 1.028 0.17063 0.79 ; N
NA 0.155 1 1.028 0.17063 0.79 ; N
NB 0.155 1 1.215 0.17063 0.79 ; N
N2 0.16 1 1.215 0.17063 0.79 ; N
N3 0.16 1 1.215 0.1625 0.79 ; N
O 0.15 1 0.926 0.148 0.85 ; O
OH 0.152 1 1.080 0.1535 0.85 ; O
O2 0.17 1 0.922 0.148 0.85 ; O
S 0.18 1 1.121 0.1775 0.96 ; S
SH 0.18 1 1.121 0.1775 0.96 ; S
*h1 0.1 1 1 0.139 0.85 ; H *
The error is "Couldn't find topology match for atomtype h1
Aborted (core dumped)"
Kindly, help
Thanks
On Tue, May 19, 2015 at 6:00 AM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Protein-Ligand complex Implicit simulation (sunita gupta)
> 2. Re: question (Mark Abraham)
> 3. Pulling a periodic molecule (for the third time) (Alex)
> 4. Re: position resrtraints (Justin Lemkul)
> 5. Re: mdp options for charmm27 force field in gromacs version
> 4.6.7 (Justin Lemkul)
> 6. Re: Protein-Ligand complex Implicit simulation (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 19 May 2015 01:05:43 +0530
> From: sunita gupta <sunita.bio at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Protein-Ligand complex Implicit simulation
> Message-ID:
> <
> CALgbHJXFX_40WEoxr3TnOR9OUkMENxeZFayXndmYSjy2Uej4-A at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello Everyone,
>
> I am trying to do protein-ligand complex simulation with implicit solvent
> parameters using gromacs. As, ligand parameters are not present in
> gbsa.itp, I added all the possible atomtypes and their van der wall radii
> from gaff ff and also managed to get get the HCT paremeters. Still its
> giving errors....Anyone please suggest me how to proceed further.
>
> Thanks in Advance
>
> --
> --
> SUNITA GUPTA
> Senior Research Fellow
> Bioinformatics Centre
> Jawaharlal Nehru University
> New Delhi- 110067
> Email- sunita.bio at gmail.com
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 18 May 2015 20:07:58 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] question
> Message-ID:
> <
> CAMNuMARsGU-m2ndLvjzjLSsiQYMwWy3txmxOc3riHw8xkvVQRA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Mon, May 18, 2015 at 9:15 PM Andrew Bostick <andrew.bostick1 at gmail.com>
> wrote:
>
> > Dear Mark
> >
> > I installed the newest version of cmake (3.2.2).
> >
> > After using cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> >
> > CUDA_TOOLKIT_ROOT_DIR not found or specified
> > -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR
> > CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is
> at
> > least version "4.0")
> > -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
> > acceleration
> > -- The GROMACS-managed build of FFTW 3 will configure with the following
> > optimizations: --enable-sse2
> > Downloading:
> > http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz
> > -- [download 100% complete]
> > CMake Error at tests/CMakeLists.txt:57 (message):
> > error: downloading
> > 'http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz'
> failed
> >
> > status_code: 1
> >
> > status_string: "Unsupported protocol"
> >
> > log: Hostname was NOT found in DNS cache
> >
> > Trying 130.237.25.133...
> >
> > Connected to gerrit.gromacs.org (130.237.25.133) port 80 (#0)
> >
> > GET /download/regressiontests-5.0.5.tar.gz HTTP/1.1
> >
> > User-Agent: curl/7.38.0
> >
> > Host: gerrit.gromacs.org
> >
> > Accept: */*
> >
> >
> >
> > HTTP/1.1 302 Found
> >
> > Date: Mon, 18 May 2015 19:11:21 GMT
> >
> > Server Apache/2.2.22 (Ubuntu) is not blacklisted
> >
> > Server: Apache/2.2.22 (Ubuntu)
> >
> > Location:
> > https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz
> >
> > Vary: Accept-Encoding
> >
> > Content-Length: 337
> >
> > Content-Type: text/html; charset=iso-8859-1
> >
> >
> >
> > Ignoring the response-body
> >
> > <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
> >
> > <html><head>
> >
> > <title>302 Found</title>
> >
> > </head><body>
> >
> > <h1>Found</h1>
> >
> > <p>The document has moved <a
> > href="
> > https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz
> > ">here</a>.</p>
> >
> >
> > <hr>
> >
> > <address>Apache/2.2.22 (Ubuntu) Server at gerrit.gromacs.org Port
> > 80</address>
> >
> > </body></html>
> >
> > Connection #0 to host gerrit.gromacs.org left intact
> >
> > Issue another request to this URL:
> > 'https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz
> '
> >
> > Protocol "https" not supported or disabled in libcurl
> >
>
> All of the above redirection is correct behaviour for our setup, but the
> problem is that your CMake is linking to an unsuitable version of libcurl.
> See http://www.cmake.org/pipermail/cmake-developers/2013-July/019430.html
> for background. You can maybe change your openssl library, file a bug with
> Ubuntu, use a Kitware-provided CMake binary, build your own, download the
> GROMACS tests yourself...
>
> Mark
>
>
> > Closing connection -1
> >
> >
> >
> > -- Configuring incomplete, errors occurred!
> > See also
> > "/export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeOutput.log".
> > See also
> > "/export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeError.log".
> >
> > ---------------------------------------------------------
> >
> > the content of CMakeOutput.log file is as follows:
> >
> > The system is: Linux - 2.6.32-431.11.2.el6.x86_64 - x86_64
> > Compiling the C compiler identification source file "CMakeCCompilerId.c"
> > succeeded.
> > Compiler: /usr/bin/cc
> > Build flags:
> > Id flags:
> >
> > The output was:
> > 0
> >
> >
> > Compilation of the C compiler identification source "CMakeCCompilerId.c"
> > produced "a.out"
> >
> > The C compiler identification is GNU, found in
> >
> >
> "/export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/3.2.2/CompilerIdC/a.out"
> >
> > Compiling the CXX compiler identification source file
> > "CMakeCXXCompilerId.cpp" succeeded.
> > Compiler: /usr/bin/c++
> > Build flags:
> > Id flags:
> >
> > The output was:
> > 0
> >
> >
> > Compilation of the CXX compiler identification source
> > "CMakeCXXCompilerId.cpp" produced "a.out"
> >
> > The CXX compiler identification is GNU, found in
> >
> >
> "/export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/3.2.2/CompilerIdCXX/a.out"
> >
> > Determining if the C compiler works passed with the following output:
> > Change Dir: /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp
> >
> > Run Build Command:"/usr/bin/gmake" "cmTryCompileExec2875484959/fast"
> > /usr/bin/gmake -f CMakeFiles/cmTryCompileExec2875484959.dir/build.make
> > CMakeFiles/cmTryCompileExec2875484959.dir/build
> > @
> > "CMakeOutput.log" 1317L, 113885C
> >
> > ----------------------------------------------------------
> > the content of CMakeError.log file is as follows:
> >
> > Performing C SOURCE FILE Test CFLAGS_EXCESS_PREC failed with the
> following
> > output:
> > Change Dir: /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp
> >
> > Run Build Command:"/usr/bin/gmake" "cmTryCompileExec2440156335/fast"
> > /usr/bin/gmake -f CMakeFiles/cmTryCompileExec2440156335.dir/build.make
> > CMakeFiles/cmTryCompileExec2440156335.dir/build
> > gmake[1]: Entering directory
> > `/state/partition1/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp'
> > /usr/local/bin/cmake -E cmake_progress_report
> > /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp/CMakeFiles 1
> > Building C object CMakeFiles/cmTryCompileExec2440156335.dir/src.c.o
> > /usr/bin/cc -DCFLAGS_EXCESS_PREC -fexcess-precision=fast -o
> > CMakeFiles/cmTryCompileExec2440156335.dir/src.c.o -c
> > /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp/src.c
> > cc1: error: unrecognized command line option "-fexcess-precision=fast"
> > gmake[1]: *** [CMakeFiles/cmTryCompileExec2440156335.dir/src.c.o] Error 1
> > gmake[1]: Leaving directory
> > `/state/partition1/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp'
> > gmake: *** [cmTryCompileExec2440156335/fast] Error 2
> >
> > Source file was:
> > int main(void) { return 0; }
> > Performing C++ SOURCE FILE Test CXXFLAGS_EXCESS_PREC failed with the
> > following output:
> > Change Dir: /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp
> >
> > Run Build Command:"/usr/bin/gmake" "cmTryCompileExec188469838/fast"
> > /usr/bin/gmake -f CMakeFiles/cmTryCompileExec188469838.dir/build.make
> > CMakeFiles/cmTryCompileExec188469838.dir/build
> > gmake[1]: Entering directory
> > `/state/partition1/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp'
> > /usr/local/bin/cmake -E cmake_progress_report
> > /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp/CMakeFiles 1
> > Building CXX object CMakeFiles/cmTryCompileExec188469838.dir/src.cxx.o
> > /usr/bin/c++ -DCXXFLAGS_EXCESS_PREC -fexcess-precision=fast -o
> > CMakeFiles/cmTryCompileExec188469838.dir/src.cxx.o -c
> > /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp/src.cxx
> > cc1plus: error: unrecognized command line option
> "-fexcess-precision=fast"
> > ---------------------------------------------------------
> >
> > How to resolve this issue?
> > Thanks in advance
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 18 May 2015 16:02:41 -0600
> From: Alex <nedomacho at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: [gmx-users] Pulling a periodic molecule (for the third time)
> Message-ID:
> <CAMJZ6qGTDQY=
> SA6Ltm5nC5jjbjnU4XzCgjwFMO5DRZa85OrSTw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi all,
>
> This is sort of my attempt to definitively conclude that what I want to do
> is not possible with the pull code.
>
> For simplicity, here's what I have: a box containing a fully periodic
> near-linear ssdna chain along Z. I want to enable non-stop translocation in
> that direction, at a constant rate.
>
> The only way I was able to make this type of translocation work is with the
> constant-force option. However, due to the peculiarities of the system,
> constant force pulling (physically, in my opinion) makes the motion
> somewhat jerky, as opposed to constant rate. At this point, I have tried
> every possible option I could find in the manual (related to the problem),
> and I just can't make it work. The most I get is a pretty energetic and
> fun-looking oscillation of the chain along Z.
>
> Do you think constant force is my only option? If someone wants to try it
> out, I can [privately] provide a tarball with the input.
>
> Any thoughts?
>
> Thanks,
>
> Alex
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 18 May 2015 20:25:05 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] position resrtraints
> Message-ID: <555A82E1.30001 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/18/15 8:47 AM, soumadwip ghosh wrote:
> > Dear Justin,
> > thanka 4 ur prompt reply. I checked that there was
> > another issue. I didnot modify the aminoacids.rtp file in order to
> > incorporate the new graphene.pdb atom types according to the force
> > field. It appears to me that the correct interaction is not arsising
> > because the atoms mentioned in the PDB file is alien to the force
> > field. Is it the case? Should I modify the aminoacids .rtp file to
>
> None of this makes any sense to me.
>
> > account for the sp2 carbon atoms and the terminal hydrogens mentioned
> > in the PDB file and then procced without really bothering about
> > pdb2gmx and position restraints? I think I made a very silly mistake
> > to begin with.
> >
>
> I really don't know how restraints factor in here. You have a suboptimal
> force
> field and an inadequate simulation time to observe the phenomenon you want.
> Those are your primary problems.
>
> -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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 18 May 2015 20:29:50 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] mdp options for charmm27 force field in
> gromacs version 4.6.7
> Message-ID: <555A83FE.1080302 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/18/15 2:21 PM, Christopher Neale wrote:
> > Dear Users:
> >
> > I would like to use the charmm27 force field in gromacs version 4.6.7
> and I would like to know if it is possible to get the proper treatment of
> vdw interactions.
> >
> > Information for gromacs 5 is here:
> > http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
> >
> > However, Gromacs 4.6.7 does not contain the option for vdw-modifier =
> force-switch
> >
> > Invalid enum 'force-switch' for variable vdw-modifier, using
> > 'Potential-shift-Verlet'
> > Next time use one of: 'Potential-shift-Verlet' 'Potential-shift'
> 'None'
> > 'Potential-switch' 'Exact-cutoff'
> >
> > Is a potential-shift the same as a force-switch and therefore the
> following options are correct for charmm27 in gromacs 4.6.7?
> >
> > ns_type = grid
> > cutoff-scheme = verlet
> > vdwtype = cut-off
> > rlist = 1.2
> > rvdw = 1.2
> > rvdw-switch = 1.0
> > rcoulomb = 1.2
> > vdw-modifier = Potential-shift-Verlet
> > coulombtype = PME
> >
> > I know this has been discussed before on the list, but I can't find
> anything that seems authoritative for gromacs versions prior to v5.
> >
>
> I cannot personally attest to anything aside from what's on the wiki. We
> have
> verified the forces are equivalent between CHARMM's vfswitch and GROMACS'
> force-switch modifier. This is how we do all our simulations, so for
> posterity,
> what I wrote on the wiki is what I must emphasize is known to be correct.
>
> From the manual, it seems that the group scheme + vdwtype = shift is
> equivalent
> to the modern force-switch modifier. The language of potential-shift does
> not
> sound as if it is the same as force-switch, and I don't know why such
> redundancy
> would be present anyway; perhaps legacy naming reasons.
>
> Any reason why you can't use 5.0 with the known correct settings? The
> check I
> would do is a single-point energy with the settings you think are
> equivalent and
> want to test and print out the forces with gmx traj.
>
> -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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 18 May 2015 20:30:32 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Protein-Ligand complex Implicit simulation
> Message-ID: <555A8428.2020703 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/18/15 3:35 PM, sunita gupta wrote:
> > Hello Everyone,
> >
> > I am trying to do protein-ligand complex simulation with implicit solvent
> > parameters using gromacs. As, ligand parameters are not present in
> > gbsa.itp, I added all the possible atomtypes and their van der wall radii
> > from gaff ff and also managed to get get the HCT paremeters. Still its
> > giving errors....Anyone please suggest me how to proceed further.
> >
>
> Without knowing what errors you're getting, the only answer is "you're
> still
> doing something wrong." Ask a generic question, get a generic answer :)
>
> -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
>
> jalemkul at 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-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 133, Issue 107
> *******************************************************
>
--
--
SUNITA GUPTA
Senior Research Fellow
Bioinformatics Centre
Jawaharlal Nehru University
New Delhi- 110067
Email- sunita.bio at gmail.com
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