[gmx-users] gromacs.org_gmx-users Digest, Vol 121, Issue 12
marzieh dehghan
dehghanmarzieh at gmail.com
Mon May 5 09:21:02 CEST 2014
Dear Justin Lemkul
Hi
thank you for your kind answer
according to your advice, we changed #include "fftest.itp" to "#include
"oplsaa.ff/fftest.itp" in the test.top.
fftest.itp contains the following cases:
; topolbuild version 1.3
; Command line:
; /home/Hossein/Desktop/topolbuild1_3/src/topolbuild -n test -dir
/home/Hossein/Desktop/topolbuild1_3/dat/gromacs -ff oplsaa
;
#define _FF_OPLS
#define _FF_OPLSAA
#define _FF_USER
[ defaults ]
;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5
#include "ffoplsaanb.itp"
test.top contains the following cases:
;
; Topology from .mol2 file
; topolbuild version 1.3
; Command line:
; /home/Hossein/Desktop/topolbuild1_3/src/topolbuild -n test -dir
/home/Hossein/Desktop/topolbuild1_3/dat/gromacs -ff oplsaa
;
; The force field files to be included
#include "oplsaa.ff/fftest.itp"
[ moleculetype ]
; name nrexcl
insulin2.pdb 3
unfortunately after writing "grompp -f ions.mdp -c test.gro -p test.top -o
ions.tpr
I confronted the new error "topology include file "oplsaa.ff/fftest.itp"
not found
I am looking forward to getting your guidance.
On Mon, May 5, 2014 at 2:17 AM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. topolbuild error (marzieh dehghan)
> 2. Re: Langevin sd integrator: wrong average temperature
> (Christopher Neale)
> 3. Re: problem still there for ACE (Justin Lemkul)
> 4. Re: topolbuild error (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 4 May 2014 23:44:59 +0430
> From: marzieh dehghan <dehghanmarzieh at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] topolbuild error
> Message-ID:
> <CA+6Z3Gm0bCTzQ04SnVLsGBfn06LBH=
> S8joGKTV8njB6SMLGh2A at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi
>
> after making topology file by using topolbuild, we used the following
> command in the gromacs:
> grompp -f em.mdp -c test_solv.gro -p test.top -o ions.tpr
>
> we confronted the following error:
> topology include file "ffoplsaanb.itp" not found
>
> would like to know how can I solve this problem?
>
> thanks in advances
>
>
> --
>
>
>
>
> *Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and
> Biophysics (IBB)University of Tehran, Tehran- Iran.*
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 4 May 2014 21:45:53 +0000
> From: Christopher Neale <chris.neale at alum.utoronto.ca>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Langevin sd integrator: wrong average
> temperature
> Message-ID: <1399239942872.96325 at alum.utoronto.ca>
> Content-Type: text/plain; charset="koi8-r"
>
> No solution here, just wanted to mention that I see this also with
> simulations of membrane proteins.
> With 4.6.1, I get a similar behaviour: actual temperature reported by
> g_energy exceeds reference temperature.
>
> Average temperatures reported are from 4 repeats of 9 us simulations after
> discarding 1 us as equilibration; stdev from 4 repeats. Reference
> temperature was 310 K.
>
> CHARMM + CHARMM lipids + Tips3p: 311.83 +/- 0.01
> Amber99SB-ILDN + S-LIPIDS + Tip3p: 311.59 +/- 0.01
> OPLS + Berger lipids + Tip4p: 310.63 +/- 0.02
>
> integrator = sd
> dt = 0.002
> constraints = all-bonds
> constraint_algorithm = lincs
> lincs-iter = 1
> lincs-order = 6
> tc_grps = System
> tau_t = 1.0
> ld_seed = -1
> ref_t = 310
>
> Chris.
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michael
> Shirts <mrshirts at gmail.com>
> Sent: 04 May 2014 14:01
> To: Discussion list for GROMACS users; Andrey Frolov
> Subject: Re: [gmx-users] Langevin sd integrator: wrong average temperature
>
> The error estimate is a rough guide, but is not always 100% accurate when
> one is making.
>
> I'd consider looking at:
>
> http://pubs.acs.org/doi/abs/10.1021/ct300688p
>
> With accompanying code here:
>
> https://github.com/shirtsgroup/checkensemble
>
> This might help ascertain a bit more how the ensemble that is being
> generates deviates from the canonical ensemble.
>
> The time step length does seemsworrisome. Perhaps you should increase the
> number of lincs iterations as well as using higher lincs order?
>
>
>
>
> On Sun, May 4, 2014 at 10:40 AM, Andrey Frolov <andrey.i.frolov at mail.ru
> >wrote:
>
> >
> > Dear Justin,
> >
> > Thank you very much for your comments.
> >
> > Sun, 04 May 2014 09:26:55 -0400 ?? Justin Lemkul <jalemkul at vt.edu>:
> > >
> > >Is the effect dependent on tau_t at all? How did you decide on a value
> > of 2.0? For larger "tau_t" the temperature is same:
> >
> > integrator,tcoupl,tau_t[ps],dt[ps] Average Err.Est. RMSD
> > Tot-Drift
> >
> >
> -------------------------------------------------------------------------------
> > sd,no,2,dt=0.002 Temperature 311.5 0.1 6.1
> > 0.6 (K)
> > sd,no,5,dt=0.002 Temperature 311.9 0.2 6.3
> > -0.1 (K)
> >
> > >
> > > Is this the correct inverse friction coefficient for supercritical
> CO2?
> > Well, I set "tau_t" according to Gromacs manual suggestion: " When [sd]
> > used as a thermostat, an appropriate value for tau-t is 2 ps, since
> this
> > results in a friction that is lower than the internal friction of water,
> > while it is high enough to remove excess heat (unless cut-off or
> > reaction-field electrostatics is used). NOTE: temperature deviations
> decay
> > twice as fast as with a Berendsen thermostat with the same tau-t"
> >
> > In this case, I aim to use Langevin dynamics as a thermostat, and
> > therefore, to my understanding, the friction coefficient should NOT
> > necessarily correspond to the experimental value. The realistic friction
> > should result itself from the interaction between molecules in the
> > simulation cell. Also, I aim to perform free energy calculations and
> > therefore the dynamics of molecules is not of the highest importance. The
> > important thing is that the sampling of the ensemble should be accurate.
> As
> > far as I can see, the change of tau_t can really change the dynamics of
> the
> > molecules, temperature and other properties relaxation times but can not
> > influence much the accuracy of the sampling. Therefore, the tau_t is set
> > arbitrary according to the manual suggestions for water.
> >
> > >I
> > >have a system I'm working with (RNA in water) and with SD the
> temperature
> > works
> > >out perfectly fine, so likely there is something specific to your system
> > that
> > >needs to be considered.
> > >
> > >Posting a full .mdp file would also be helpful. Though you have listed
> > most of
> > >the important settings, seeing everything is often useful for diagnostic
> > purposes.
> > ; RUN CONTROL PARAMETERS =
> > integrator = sd ; changed by FillMDP.sh
> > ; start time and timestep in ps =
> > tinit = 0
> > dt = 0.002
> > ; 6 ns - enought to sample small molecules (without slow internal degrees
> > of freedom) [Shirts et al.]
> > nsteps = 2500000 ; changed by FillMDP.sh
> > ; mode for center of mass motion removal =
> > ; We remove center of mass motion. In periodic boundary conditions, the
> > center of mass motion is spurious; the periodic system is the same in all
> > translational directions.
> > comm-mode = Linear
> > ; number of steps for center of mass motion removal =
> > nstcomm = 1
> > ; OUTPUT CONTROL OPTIONS =
> > nstlog = 1000
> > nstenergy = 100 ; changed by FillMDP.sh
> > nstxout = 100000
> > nstvout = 100000
> > nstfout = 0
> > nstxtcout = 10000 ; changed by FillMDP.sh
> > xtc_precision = 100000 ; changed by FillMDP.sh
> > xtc_grps =
> > ; NEIGHBORSEARCHING PARAMETERS =
> > ; nblist update frequency =
> > nstlist = 10
> > ; ns algorithm (simple or grid) =
> > ns_type = grid
> > ; Periodic boundary conditions: xyz or no =
> > pbc = xyz
> > ; Neighbor list should be at least 2 A greater than the either rcut or
> rvdw
> > ; nblist cut-off =
> > rlist = 1.4
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW: These parameters were all optimized
> > for fast and accurate small molecule calculations.
> > ; See Shirts and Paliwal (2011)
> > ; Method for doing electrostatics =
> > coulombtype = PME-Switch
> > rcoulomb-switch = 1.19999999
> > rcoulomb = 1.2
> > ; Method for doing Van der Waals =
> > vdw-type = Switch
> > ; cut-off lengths =
> > rvdw-switch = 1.0
> > rvdw = 1.2
> > ; Spacing for the PME/PPPM FFT grid =
> > fourierspacing = 0.1
> > ; EWALD/PME/PPPM parameters =
> > pme_order = 6
> > ewald_rtol = 1e-06
> > ewald_geometry = 3d
> > epsilon_surface = 0
> > ; Apply long range dispersion corrections for Energy and Pressure =
> > DispCorr = EnerPres
> >
> > ; Temperature coupling
> > ; Groups to couple separately =
> > tcoupl = no ; changed by FillMDP.sh
> > tc-grps = System
> > ; Time constant (ps) and reference temperature (K) =
> > ; for equilibration - strong thermostat coupling
> > tau_t = 2 ; changed by FillMDP.sh
> > ref_t = 308.15 ; changed by FillMDP.sh
> > ; Pressure coupling =
> > ;;; use Berendsen ONLY for equilibration run
> > pcoupl = no
> > ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
> > ; for equilibration - strong barostat coupling
> > tau_p = 1.0
> > compressibility = 4.5e-5
> > ref_p = 250.0 ; changed by FillMDP.sh
> > ; We don't strictly need these, because it already has velocities
> > ; that are at the right temperature. But including this is safer.
> > ----------
> > gen_vel = yes
> > gen_temp = 308.15 ; changed by FillMDP.sh
> > gen_seed = 12 ; make sure you set the seed to be able to reproduce the
> > simulation
> >
> > ;;; This contraints section taken from ethanol solvation example on
> > alchemistry.org
> > ;; constrain the hydrogen bonds, allowing longer timesteps.
> > ;; Better to choose a higher lincs order just to be sure that
> > ;; the constraints are obeyed to high precision; it's not that expensive.
> > constraints = hbonds
> > ;; Type of constraint algorithm =
> > constraint-algorithm = lincs
> > ;; Highest order in the expansion of the constraint coupling matrix =
> > lincs-order = 12
> >
> > Andrey
> >
> >
> >
> > >
> > >-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
> > >
> > >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.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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>
> ------------------------------
>
> Message: 3
> Date: Sun, 04 May 2014 17:44:58 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] problem still there for ACE
> Message-ID: <5366B4DA.4080100 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 5/4/14, 3:06 PM, Albert wrote:
> > Hello:
> >
> > I capped the protein with residues ACE and NMA at N-ter and C-ter
> respectively.
> > Here is the coordinate:
> >
> > ATOM 1 CH3 ACE X 38 9.945 21.608 90.016 1.00 0.00
> C
> > ATOM 4 HH31HACE X 38 10.267 21.376 91.056 1.00 0.00
> H
> > ATOM 5 HH32HACE X 38 9.614 22.669 89.956 1.00 0.00
> H
> > ATOM 6 HH33HACE X 38 9.095 20.947 89.733 1.00 0.00
> H
> > ATOM 2 C ACE X 38 11.113 21.380 89.058 1.00 0.00
> C
> > ATOM 3 O ACE X 38 12.196 20.997 89.497 1.00 0.00
> O
> > ATOM 4 N GLY X 39 10.957 21.602 87.705 1.00 0.00
> N
> > ATOM 5 CA GLY X 39 12.077 21.382 86.795 1.00 0.00
> C
> > ATOM 6 C GLY X 39 11.787 21.661 85.315 1.00 0.00
> C
> > ATOM 7 O GLY X 39 12.527 21.182 84.455 1.00 0.00
> O
> >
> > ....
> >
> > ATOM 2309 N LYS X 335 38.981 11.135 41.177 1.00 0.00
> N
> > ATOM 2310 CA LYS X 335 40.402 10.845 41.347 1.00 0.00
> C
> > ATOM 2311 C LYS X 335 40.881 11.426 42.687 1.00 0.00
> C
> > ATOM 2312 O LYS X 335 41.551 12.456 42.677 1.00 0.00
> O
> > ATOM 2313 CB LYS X 335 41.191 11.366 40.117 1.00 0.00
> C
> > ATOM 2314 CG LYS X 335 40.902 10.605 38.817 1.00 0.00
> C
> > ATOM 2315 CD LYS X 335 41.781 11.075 37.647 1.00 0.00
> C
> > ATOM 2316 CE LYS X 335 41.492 10.315 36.347 1.00 0.00
> C
> > ATOM 2317 NZ LYS X 335 42.382 10.755 35.267 1.00 0.00
> N1+
> > ATOM 4782 N NMA X 335 40.573 10.815 43.885 1.00 0.00
> N
> > ATOM 4784 H NMA X 335 40.023 9.969 43.894 1.00 0.00
> H
> > ATOM 4783 CH3 NMA X 335 41.042 11.390 45.138 1.00 0.00
> C
> > ATOM 4785 HH31 NMA X 335 41.625 12.311 44.913 1.00 0.00
> H
> > ATOM 4786 HH32 NMA X 335 40.172 11.644 45.784 1.00 0.00
> H
> > ATOM 4787 HH33 NMA X 335 41.688 10.657 45.670 1.00 0.00
> H
> > END
> >
> >
> >
> > When I try to run command:
> >
> > pdb2gmx -f p.pdb -o gmx.pdb -ter
> >
> > Select start terminus type for ACE-38
> > 0: NH3+
> > 1: NH2
> > 2: 5TER
> > 3: None
> > 3
> > Start terminus ACE-38: None
> > Select end terminus type for LYS-335
> > 0: COO-
> > 1: COOH
> > 2: CT2
> > 3: 3TER
> > 4: None
> > 4
> > End terminus LYS-335: None
> >
> > -------------------------------------------------------
> > Program pdb2gmx, VERSION 4.6.5
> > Source code file: /home/albert/gromacs-4.6.5/src/kernel/pdb2top.c, line:
> 1109
> >
> > Fatal error:
> > There is a dangling bond at at least one of the terminal ends. Fix your
> > coordinate file, add a new terminal database entry (.tdb), or select the
> proper
> > existing terminal entry.
> >
> >
> > When I run command:
> >
> > pdb2gmx -f p.pdb -o gmx.pdb
> >
> > Fatal error:
> > atom N not found in buiding block 1ACE while combining tdb and rtp
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> >
> > I noticed this thread:
> > https://www.mail-archive.com/gmx-users@gromacs.org/msg49517.html
> >
> > and Justine said there is a N atom on ACE instead of the first atom of
> the next
> > residue. However, as shown in my coordinate, there is NO atom N in ACE
> at all.
> > And I cannot figure out what's the problem....
> >
>
> No, what I said in that thread is that the OP had constructed ACE
> incorrectly
> such that it contained an N that shouldn't be there. There should indeed
> not be
> any N atom in ACE. The second approach is simply incorrect; you need to
> interactively select termini when using capping groups. The first
> approach was
> completely correct, but note that the problem is not with ACE, it is with
> NMA.
> pdb2gmx is finding LYS as the terminus instead of NMA, and when you tell
> pdb2gmx
> to apply to terminus, LYS has a dangling (incomplete) end. Likely this
> stems
> from the fact that residuetypes.dat does not, by default, include NMA as a
> Protein residue, so pdb2gmx finds a Protein chain from ACE38 - LYS335,
> then a
> separate Other chain of NMA. Adding NMA to residuetypes.dat and repeating
> the
> first approach will solve the 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 04 May 2014 17:46:13 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] topolbuild error
> Message-ID: <5366B525.3090808 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 5/4/14, 3:14 PM, marzieh dehghan wrote:
> > Hi
> >
> > after making topology file by using topolbuild, we used the following
> > command in the gromacs:
> > grompp -f em.mdp -c test_solv.gro -p test.top -o ions.tpr
> >
> > we confronted the following error:
> > topology include file "ffoplsaanb.itp" not found
> >
> > would like to know how can I solve this problem?
> >
>
> Such nomenclature went away with the release of Gromacs 4.5, in which the
> force
> field files were reorganized and renamed. Adapt the topology to the new
> organization, i.e. "#include oplsaa.ff/forcefield.itp"
>
> -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
>
> 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 121, Issue 12
> ******************************************************
>
--
*Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and
Biophysics (IBB)University of Tehran, Tehran- Iran.*
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