[gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system
> Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > >1. Re: Re: change in rename of 1POPC to 1LIG thoughcoordinate > and atom same in 1LIG of 1POPC, during solvation of system > (Justin A. Lemkul) >2. Segmentation fault - pdb2gmx specbond.dat (Steven Neumann) >3. energy conservation: shift vs shifted user potential > (Anja Kuhnhold) >4. Cannot get correct pressure value with MTTK pressurecoupling > (Bao Kai) >5. Re: Cannot get correct pressure value with MTTK pressure > coupling (Justin A. Lemkul) > > > -- > > Message: 1 > Date: Wed, 06 Jun 2012 08:56:04 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] Re: change in rename of 1POPC to 1LIG though > coordinate and atom same in 1LIG of 1POPC, during solvation of system > To: Discussion list for GROMACS users > Message-ID: <4fcf5364....@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > On 6/6/12 8:52 AM, Sangita Kachhap wrote: > >>> On 6/6/12 3:09 AM, Sangita Kachhap wrote: >>>> >>>> Hello all >>>> I have to do MD simulation of membrane protein having docked ligand in POPC >>>> lipid bilayer. >>>> I am geeting error during solvation of system: >>>> Resname of 1POPC in system_shrink1.gro converted into 1LIG >>>> >>>> >>>> I have done following: >>>> >>>> GROMACS COMMAND >>>> >>>> 1) Generate topol.top using GROMOS96 53A6 parameter set >>>> pdb2gmx -f 3gd8-mod.pdb -o 3gd8-mod-processed.gro -water spc >>>> >>>> >>>> at prompt select 14 >>>> >>>> 2) Download: >>>> * popc128.pdb - the structure of a 128-lipid POPC bilayer >>>> * popc.itp - the moleculetype definition for POPC >>>> * lipid.itp - Berger lipid parameters >>>> >>>> from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies >>>> >>>> 3) Modify topol.top with: >>>> #include "gromos53a6.ff/forcefield.itp" >>>> >>>> to: >>>> >>>> #include "gromos53a6_lipid.ff/forcefield.itp" >>>> >>>> >>>> & >>>> >>>> ; Include Position restraint file >>>> #ifdef POSRES >>>> #include "posre.itp" >>>> #endif >>>> ; Include ligand topology >>>> #include "ligand-full.itp" >>>> >>>> ; Include POPC chain topology >>>> #include "popc.itp" >>>> >>>> ; Include water topology >>>> #include "gromos53a6_lipid.ff/spc.itp" >>>> >>>> and at the end add LIG 1 in [molecules] >>>> >>>> 4) cp files >>>> aminoacids.rtp >>>> aminoacids.hdb >>>> aminoacids.c.tdb >>>> aminoacids.n.tdb >>>> aminoacids.r2b >>>> aminoacids.vsd >>>> ff_dum.itp >>>> ffnonbonded.itp >>>> ffbonded.itp >>>> forcefield.itp >>>> ions.itp >>>> spc.itp >>>> watermodels.dat >>>> >>>> from gromacs top to directory named gromos53a6_lipid.ff in working >>>> directory. >>>> Append parameter ([ atomtypes ], [ nonbond_params ], and [ pairtypes ])from >>>> lipid.itp to ffnonbonded.itp& ffbonded.itp and create a forcefield.doc >>>> file >>>> that contains a description of the force field parameters contain "GROMOS96 >>>> 53A6 >>>> force field, extended to include Berger lipid parameters". >>>> Delete line ";; parameters for lipid-GROMOS interactions." and its >>>> subsequent >>>> line, change HW as H of [ nonbond_params ] >>>> >>>> >>>> 5) Generate .tpr for POPC >>>> grompp -f minim
[gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system
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>
>1. Re: Question regarding genion (Justin A. Lemkul)
>2. Re: change in rename of 1POPC to 1LIG though coordinate and
> atom same in 1LIG of 1POPC, during solvation of system
> (Justin A. Lemkul)
>3. Re: Scaling/performance on Gromacs 4 (Manu Vajpai)
>4. Atomtype OW_tip4p not found (Amir Abbasi)
>
>
> --
>
> Message: 1
> Date: Wed, 06 Jun 2012 06:04:43 -0400
> From: "Justin A. Lemkul"
> Subject: Re: [gmx-users] Question regarding genion
> To: Discussion list for GROMACS users
> Message-ID: <4fcf2b3b.30...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>
>
>
> On 6/6/12 5:38 AM, Matthias Ernst wrote:
>> Hi,
>>
>> I have to questions regarding genion.
>>
>> 1) Is there a possibility to tell genion in advance which group of molecules
>> to
>> replace by ions (for me, solvent is always the choice so I want to skript it
>> but
>> I did not find any parameters for this)?
>>
>
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
>
>> 2) I want to neutralize a charged system. Therefore, as I found out, I can
>> use
>> the -neutral option. But it seems to me that this option does not work if I
>> do
>> not specify a concentration (system has a charge of -52):
>> genion -s system_in_solvent.tpr -o solventions.gro -p topol_water.top
>> -neutral
>> [snap]
>> Reading file system_in_solvent.tpr, VERSION 4.5.4 (single precision)
>> Using a coulomb cut-off of 1 nm
>> No ions to add and no potential to calculate.
>>
>> If I use genion {parameters as above} -conc 0.0 it also won't add ions but if
>> I
>> try e.g. genion {parameters as above} -c 0.0001, it will add 52 NA and 0 CL
>> ions
>> which corresponds to a neutral system (with -c 0.001, it will add 53 NA and 1
>> CL
>> ions, meaning resulting salt concentration is > 0). I use the amber99sb
>> forcefield.
>> Is this behaviour desired and do I miss the point of the -neutral option not
>> working without specifying a concentration?
>>
>
> I have also found that -neutral must always be used in conjunction with -conc.
> It would be nice if this were not the case.
>
> -Justin
>
> --
>
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
>
>
> ----------
>
> Message: 2
> Date: Wed, 06 Jun 2012 06:08:55 -0400
> From: "Justin A. Lemkul"
> Subject: Re: [gmx-users] change in rename of 1POPC to 1LIG though
> coordinate and atom same in 1LIG of 1POPC, during solvation of
> system
> To: Discussion list for GROMACS users
> Message-ID: <4fcf2c37.4040...@vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> On 6/6/12 3:09 AM, Sangita Kachhap wrote:
>>
>> Hello all
>> I have to do MD simulation of membrane protein having docked ligand in POPC
>> lipid bilayer.
>> I am geeting error during solvation of system:
>> Resname of 1POPC in system_shrink1.gro converted into 1LIG
>>
>>
>> I have done following:
>>
>> GROMACS COMMAND
>>
>> 1) Generate topol.top using GROMOS96 53A6 parameter set
>> pdb2gmx -f 3gd8-mod.pdb -o 3gd8-mod-processed.gro -water spc
>>
>>
>> at prompt select 14
>>
>> 2) Download:
>> * popc128.pdb - the structure of a 128-lipid POPC bilayer
>> * popc.itp - the moleculetype definition for POPC
>> * lipid.itp - Berger lipid parameters
>>
>> from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
>>
>> 3) Modify topol.top with:
>> #include "gromos53a6.ff/forcefield.itp"
>>
>> to:
>>
>> #include "gromos53a6_lipid.ff/fo
[gmx-users] change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system
Hello all I have to do MD simulation of membrane protein having docked ligand in POPC lipid bilayer. I am geeting error during solvation of system: Resname of 1POPC in system_shrink1.gro converted into 1LIG I have done following: GROMACS COMMAND 1) Generate topol.top using GROMOS96 53A6 parameter set pdb2gmx -f 3gd8-mod.pdb -o 3gd8-mod-processed.gro -water spc at prompt select 14 2) Download: * popc128.pdb - the structure of a 128-lipid POPC bilayer * popc.itp - the moleculetype definition for POPC * lipid.itp - Berger lipid parameters from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies 3) Modify topol.top with: #include "gromos53a6.ff/forcefield.itp" to: #include "gromos53a6_lipid.ff/forcefield.itp" & ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include ligand topology #include "ligand-full.itp" ; Include POPC chain topology #include "popc.itp" ; Include water topology #include "gromos53a6_lipid.ff/spc.itp" and at the end add LIG 1 in [molecules] 4) cp files aminoacids.rtp aminoacids.hdb aminoacids.c.tdb aminoacids.n.tdb aminoacids.r2b aminoacids.vsd ff_dum.itp ffnonbonded.itp ffbonded.itp forcefield.itp ions.itp spc.itp watermodels.dat from gromacs top to directory named gromos53a6_lipid.ff in working directory. Append parameter ([ atomtypes ], [ nonbond_params ], and [ pairtypes ])from lipid.itp to ffnonbonded.itp & ffbonded.itp and create a forcefield.doc file that contains a description of the force field parameters contain "GROMOS96 53A6 force field, extended to include Berger lipid parameters". Delete line ";; parameters for lipid-GROMOS interactions." and its subsequent line, change HW as H of [ nonbond_params ] 5) Generate .tpr for POPC grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr -maxwarn 1 (change OW1, HW2, HW3 to OW, HW and HW2 respectively) 6) Remove periodicity trjconv -s em.tpr -f popc128a.pdb -o popc128a_whole.gro -pbc mol -ur compact (at command prompt select 0) 7) Oriant the protein within the same coordinate as written in end of popc128a_whole.gro editconf -f 3gd8-mod-processed.gro -o 3gd8-mod-processe_newbox.gro -c -box 6.23910 6.17970 6.91950 8) Pack lipid around protein cat 3gd8-mod-processe_newbox.gro popc128a_whole.gro > system.gro Remove unnecessary lines (the box vectors from the KALP structure, the header information from the DPPC structure and update the second line of the coordinate file (total number of atoms) accordingly. 9) Modify topol.top to add positional restrain on protein ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include "strong_posre.itp" #endif ; Include DPPC chain topology #include "dppc.itp" ; Include water topology #include "gromos53a6_lipid.ff/spc.itp" & Genrate new positional restraint genrestr -f 3gd8-mod-processe_newbox.gro -o strong_posre.itp -fc 10 10 10 for system (protein + ligand) Add a line "define = -DSTRONG_POSRES" to .mdp file 10) addion POPC 128 to topol.top 11) Scale down lipid perl inflategro.pl system.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat 12) Solvate with water Copy vdwradii.dat from Gromacs top to working directory and change the value of C from 0.15 to 0.375(to avoid addition of water in lipid hydrohphobic core) genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro -p topol.top Upto 11th step .gro file is OK conatin protein resid 32-254, ligand 1LIG, POPC resid 1-128 and solvent After 12th step in gro file protein is there 32-254, Ligand 1LIG but POPC resid 2-128 because resid 1 of POPC is converted to 1LIG though all cordinate and atom name are same of 1POPC in 1LIG. Anybody please suggest me why this change in rename is occuring. With regards __ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to get md_0_2. prefix for all output files during entexding production run, like got during first run md_0_1.
> Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > >1. Re: How to get md_0_2. prefix for all output files during > entexding production run, like got during first run md_0_1. > (Justin A. Lemkul) >2. Re: Fatal error: No atoms found in .rtp file in residue pairs > (Justin A. Lemkul) >3. Re: Fatal error: No atoms found in .rtp file in residue pairs > (Shima Arasteh) > > > -- > > Message: 1 > Date: Sun, 13 May 2012 13:12:37 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] How to get md_0_2. prefix for all output > files duringentexding production run, like got during first run > md_0_1. > To: Discussion list for GROMACS users > Message-ID: <4fafeb85.20...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > On 5/13/12 12:52 PM, Sangita Kachhap wrote: >> Hello all >> >> I am running GROMACS Tutorial: KALP15 in POPC >> I have compeleted production run 1 ns now I want to extend it for next 1 ns. >> For this I have used commond: >> >> tpbconv -s md_0_1.tpr -extend 1000 -o md_0_2.tpr >> mdrun -s nmd_0_2.tpr -cpi md_0_1.cpt >> >> I am getting files are: >> ener.edr >> md.log >> state.cpt >> state_prev.cpt >> traj.trr >> traj.xtc >> confout.gro >> >> During first 1 ns production I have got all files with prefix md_0_1. >> How I can get it (prefix md_0_2. for all the above files)in next 1 ns >> production >> run. >> >> Anyone please suggest. >> > > Note the use of -deffnm in the tutorial to set default output names. If you > want your files to be called "md_0_2.(extension)" then you need to run: > > mdrun -deffnm md_0_2 -cpi md_0_1.cpt Thanks for reply its running fine now. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > -- > > Message: 2 > Date: Sun, 13 May 2012 13:14:30 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in > residue pairs > To: Discussion list for GROMACS users > Message-ID: <4fafebf6.8040...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 5/13/12 1:06 PM, Shima Arasteh wrote: >> Even in gromos87, if I want to make a .rtp file for formyl, I need to put H >> atom >> in it? I mean, defining all atoms of a residue is necessary? Aren't the >> hydrogen >> atoms set by the gromacs package? >> > > No. The presence of hydrogen atoms is set by the force field, not the > software > that makes use of the force fields. In the Gromos force fields (and I > certainly > hope you're not using Gromos87, as it is ancient and better options are > available), polar H atoms are explicitly represented. In the case of an > aldehyde, I would strongly suspect you need an explicit H. I believe there > have > been recent publications regarding extensions of Gromos96 (note, NOT Gromos87) > that include such organic groups. Using those parameters may speed your > progress. If my recollection is incorrect and such parameters do not exist, > you > need to derive them yourself. > > -Justin > >> Cheers, >> Shima >> >> >> *From:* Justin A. Lemkul >> *To:* Discussion list for GROMACS users >> *Sent:* Sunday, May 13, 2012 8:36 PM >> *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in >> residue >> pairs >> >> >> >> On 5/13/12 11:43 AM, Shima Arasteh wrote: >> > Again thanks for all your replies. >> > As I got through your advices, I found that the atoms contribute in making >> bonds >> &
[gmx-users] How to get md_0_2. prefix for all output files during entexding production run, like got during first run md_0_1.
Hello all I am running GROMACS Tutorial: KALP15 in POPC I have compeleted production run 1 ns now I want to extend it for next 1 ns. For this I have used commond: tpbconv -s md_0_1.tpr -extend 1000 -o md_0_2.tpr mdrun -s nmd_0_2.tpr -cpi md_0_1.cpt I am getting files are: ener.edr md.log state.cpt state_prev.cpt traj.trr traj.xtc confout.gro During first 1 ns production I have got all files with prefix md_0_1. How I can get it (prefix md_0_2. for all the above files)in next 1 ns production run. Anyone please suggest. With regards Sangita Kachhap SRF BIC,IMTECH CHANDIGARH __ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] solvent group size (12548) is not a multiple of 3
> Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > >1. Re: keep the nanotube cylindrical. (Elton Carvalho) >2. poor performance in Hemiltonian Replica Exchange (francesco oteri) >3. Re: poor performance in Hemiltonian Replica Exchange > (Michael Shirts) >4. solvent group size (12548) is not a multiple of 3 > (Sangita Kachhap) >5. rvdw and DispCorr (Bernhard Knapp) >6. Re: solvent group size (12548) is not a multiple of 3 (Terry) > > > -- > > Message: 1 > Date: Thu, 10 May 2012 16:21:31 +0200 > From: Elton Carvalho > Subject: Re: [gmx-users] keep the nanotube cylindrical. > To: Za Pour , Discussion list for GROMACS users > > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > On Sat, May 5, 2012 at 7:27 PM, Za Pour wrote: >> Dear gmx users >> I am simulation a system including carbon nanotube+water.I have done these >> things: >> However as I looked into the nvt.gro I realized that the cylindrical shape >> of carbon nanotube >> ?has been changed.I am not sure what I have done is correct or not?and how >> to keep nanotube cylindrical ? any help would be really appreciated. >> ? Best regards > > I had a similar issue, but I modeled the CNT carbon atoms as opls_147, > trying not to change the parameters too much, so I kept the bond > lengths, angles and force constants untouched. > > I noticed that removing the [ dihedrals ] section from the resulting > topology significantly reduced the tube deformation. Since g_x2top > doesn't generate impropers and a CNT has no rotable bonds, these > dihedrals are spurious, anyway. > > Also, do your tubes have open ends? If you can afford to have periodic > tubes, so that the box z length is a multiple of the tube unit cell > and the tube ends are bonded through the box wall, it seems much more > stable. > Or you could try capped tubes. > > > -- > Elton Carvalho > Tel.: +55 11 3091-6985/6922 > Dept F?sica dos Materiais e Mec?nica > Instituto de F?sica > Universidade de S?o Paulo > P.O. Box 66318 - 05314-970 S?o Paulo-SP, Brazil > > > -- > > Message: 2 > Date: Thu, 10 May 2012 18:23:54 +0200 > From: francesco oteri > Subject: [gmx-users] poor performance in Hemiltonian Replica Exchange > To: Discussion list for GROMACS users > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear gromacs users, > > I performed a Hemiltonian Replica Exchange (i.e. replica exchange where > each replica has a init_lambda=0, delta_lambda=0 and init_lambda ranging > uniformely from 0 to 1). > > Since I have only ten fixed discrete lambda, I run a Temperature Replica > Exchange where, for each replica I generated a .top file with the parameter > rescaled through a > python script ( in practice I did through python the same thing gromacs is > supposed to do with the H-REM previously described). Now gromacs complained > because > every replica has the same setup, so I changed the temperatures using very > close values (300.0001K, > 300.0002K,300.0003K,300.0004K,300.0005K,300.0006K,300.0007K,300.0008K, > 300.0009K) > With this setup the simulation runs fine and I expect to have similar > result. > > Then I compared the results observing two phenomena: > > 1) In the second case exchange rate is 100%, while in the first case I have > an exchange rate close to 30%. > Does it rise because the temperatures are too close? > > 2) The second setup is 3x faster! > In particular I observe an imbalance between PME and force calculation > ranging from 10% to 60%. > I tried to run each replia indipendently (a different mdrun instance for > each .tpr file) but still I observe the same performance slowdown. > I guess the free energy impairs the efficient force calculation, but I dont > understand why. > > Can someone explain me the two observations? > > > > Francesco > -- next part -- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attach
[gmx-users] solvent group size (12548) is not a multiple of 3
Hello all I am runing Gromacs Tutorial KALP-15 in DPPC (I am using POPC) I am geeting error during addiotion of ions Fatal error: Your solvent group size (12548) is not a multiple of 3 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I have done following: GROMACS COMMAND 1) Generate topol.top using GROMOS96 53A6 parameter set pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc ay prompt select 13, 2, 2 2) Download: * dppc128.pdb - the structure of a 128-lipid DPPC bilayer * dppc.itp - the moleculetype definition for DPPC * lipid.itp - Berger lipid parameters from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies 3) Modify topol.top with: #include "gromos53a6.ff/forcefield.itp" to: #include "gromos53a6_lipid.ff/forcefield.itp" & ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include POPC chain topology #include "popc.itp" ; Include water topology #include "gromos53a6_lipid.ff/spc.itp" 4) cp files aminoacids.rtp aminoacids.hdb aminoacids.c.tdb aminoacids.n.tdb aminoacids.r2b aminoacids.vsd ff_dum.itp ffnonbonded.itp ffbonded.itp forcefield.itp ions.itp spc.itp watermodels.dat from gromacs top to directory named gromos53a6_lipid.ff in working directory. Append parameter ([ atomtypes ], [ nonbond_params ], and [ pairtypes ])from lipid.itp to ffnonbonded.itp & ffbonded.itp and create a forcefield.doc file that contains a description of the force field parameters contain "GROMOS96 53A6 force field, extended to include Berger lipid parameters". Delete line ";; parameters for lipid-GROMOS interactions." and its subsequent line, change HW as H of [ nonbond_params ] 5) Generate .tpr for POPC grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr -maxwarn 1 (change OW1, HW2, HW3 to OW, HW and HW2 respectively) 6) Remove periodicity trjconv -s em.tpr -f popc128a.pdb -o popc128a_whole.gro -pbc mol -ur compact (at command prompt select 0) 7) Oriant the KALP peptide within the same coordinate as written in end of popc128a_whole.gro editconf -f KALP-15_processed.gro -o KALP_newbox.gro -c -box 6.23910 6.17970 6.91950 8) Pack lipid around protein cat KALP_newbox.gro popc128a_whole.gro > system.gro Remove unnecessary lines (the box vectors from the KALP structure, the header information from the DPPC structure) and update the second line of the coordinate file (total number of atoms) accordingly. 9) Modify topol.top to add positional restrain on protein ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include "strong_posre.itp" #endif ; Include DPPC chain topology #include "dppc.itp" ; Include water topology #include "gromos53a6_lipid.ff/spc.itp" & Genrate new positional restraint genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 (at prompt select 2) Add a line "define = -DSTRONG_POSRES" to .mdp file 10) Scale down lipid perl inflategro.pl system.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat system_shrink1.gro 11) addion POPC 128 to topol.top 12) Solvate with water Copy vdwradii.dat from Gromacs top to working directory and change the value of C from 0.15 to 0.375(to avoid addition of water in lipid hydrohphobic core) genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro -p topol.top grompp -f ions.mdp -c system_shrink1_solv.gro -p topol.top -o ions.tpr genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname CL -nn 4 (at command prompt select 0) So can anyone please help me correct this error. With regards Sangita Kachhap SRF BIC,IMTECH CHANDIGARH __ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Nubmer of coordinate not matching in topol.top and sol.gro
s not work well.
>
> Here my part of run parameters about the Constraint in my mdp file
>
> ##
>
> constraints = all-bonds; hbonds; all-bonds
> constraint-algorithm = Lincs
>
> pull??? = constraint
> pull_geometry?? = distance
> pull_dim??? = N N Y
> pull_ngroups??? = 1
> pull_group0 = Surface
> pull_group1 = Protein
> pull_nstxout??? = 1000
> pull_nstfout??? = 1000
> pull_rate1? = -0.001
> pull_init1? = 1.73331
> ##
>
> Based my understanding, the pull_rate1 is about -0.001/ps.
> That means in the pullx.xvg file, the distance shoud be as follows (only the
> z-distance shown, time step is 1fs.)
> 1.73331
> 1.72231
> 1.72131
> 1.72031
> .
> .
> However, in my simulation, the results from the simulation is as follow:
> 1.73331
> 1.71154
> 1.75043
> 1.73213
> 1.78065
> 1.79769
> 1.84298
> 1.87008
>
> It seems some force has been imposed on the pull molecules.
> But in the pullf.xvg the force is ZERO.
> I used the latest gromacs version, But for the gromacs4.0 it works very well
> (works as what I think).
> Can someone help me about the issue?
>
> Thanks a lot
>
> Jerry
>
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20120502/97b52262/attachment-0001.html
>
> --
>
> Message: 5
> Date: Wed, 02 May 2012 13:43:18 -0400
> From: "Justin A. Lemkul"
> Subject: Re: [gmx-users] Number of cooredinate in topol.top and
> solv.gro notmatching
> To: Discussion list for GROMACS users
> Message-ID: <4fa17236.3040...@vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> On 5/2/12 1:09 PM, Sangita Kachhap wrote:
>
>>>> I have to do MD simulation of ligand bound membrane protein in lipid
>>>> bilayer.
>>>> Thus I am doing tutorialfor Protein - Ligand tutorial:
>>>>
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
>>>>
>>>> I have used following command:
>>>>
>>>> pdb2gmx -f 3HTB_clean.pdb -o conf.gro -water spc
>>>>
>>>> editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
>>>>
>>>> genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
>>>>
>>>> grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
>>>>
>>>> I am getting stuck at last command. Its showing following error:
>>>>
>>>> Fatal error:
>>>> number of coordinates in coordinate file (solv.gro, 33049)
>>>>does not match topology (topol.top, 33064)
>>>> For more information and tips for troubleshooting, please check the GROMACS
>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>
>>>
>>> Did you follow the link? Did you read
>>> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>>> ?
>>>
>>>> {But when I calculate number of atom in topol.top and solv.gro it is same}
>>>>
>>>
>>> That's not possible.
>>>
>>>> When I checked above http: I got that such type of error may be due to cpp
>>>> variable is not properly set in the .mdp file.
>>>> But When I locate ccp in my system and add it to .mdp file.
>>>>
>>>> "
>>>> ; LINES STARTING WITH ';' ARE COMMENTS
>>>> title = Minimization ; Title of run
>>>> cpp =/usr/bin/cpp
>>>> ; Parameters describing what to do, when to stop and what to save
>>>> "
>>>>
>>>> Then also it showing same error.
>>>>
>>>> Please help me to solve this problem.
>>>>
>>>> I am using gromacs-4.5.5 and installed with fftw-3.3.1 .
>>>>
>>>
>>> The cpp parameter is ignored for all Gromacs versions as of 4.5.
>>>
>>> Your problem is that you don't have a ligand in your coordinate file. Note
>>> that
>>> you're off by 15 atoms, which is exactly how many are in the ligand
>>> described
>>> in
>>> the tutorial. Go back and read the instructions closely, as appending the
>>> ligand to the protein coordinate file is discussed in detail.
>>
>>
>>
>> Thanks for
[gmx-users] Number of cooredinate in topol.top and solv.gro not matching
> Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > >1. Re: How to remove H atom from residue in gro file? > (Justin A. Lemkul) >2. Re: How to remove H atom from residue in gro file? (Mark Abraham) >3. Re: Number of coordinate in topol.top and solv.gro not > matching (Justin A. Lemkul) >4. Re: Automation of selecting water around a molecule (Mark Abraham) >5. ? (Shima Arasteh) >6. Re: GROMOS87 and CHARMM27 (Justin A. Lemkul) > > > -- > > Message: 1 > Date: Wed, 02 May 2012 09:09:39 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] How to remove H atom from residue in gro > file? > To: Discussion list for GROMACS users > Message-ID: <4fa13213.2040...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 5/2/12 6:55 AM, Hagit G wrote: >> Hi gmx users, >> >> >> Well, I saw this question but the answer was not understood. >> I'm trying to work with the file 1PPB.pdb. There are 2 chains connected with >> a >> disulfide bond. Gromacs automatically adds H atoms. >> Although the disulfide bond is there, Gromacs ignore it because *each cystein >> is >> on a different chain*. So it adds H and therefor the disulfide bond is ruined >> during energy minimization. >> Is there any way to recreate such a disulfide bond (Please don't tell me >> again >> about "-ss" it works only on one chain. Moreover, the bond is existed on the >> pdf >> file.) or never ruined it at the first place? >> > > Well you may need to use -ss, but since you don't want to hear about it, I > won't > say anything more... > > What you need to do is create a [moleculetype] that consists of both chains. > The pdb2gmx option -chainsep will allow you to create a properly merged > molecule > that can form the intermolecular disulfide because the two molecules will be > considered as one [moleculetype], as Gromacs requires. > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > -- > > Message: 2 > Date: Wed, 02 May 2012 23:11:08 +1000 > From: Mark Abraham > Subject: Re: [gmx-users] How to remove H atom from residue in gro > file? > To: Discussion list for GROMACS users > Message-ID: <4fa1326c.6080...@anu.edu.au> > Content-Type: text/plain; charset="iso-8859-1" > > On 2/05/2012 8:55 PM, Hagit G wrote: >> Hi gmx users, >> >> Well, I saw this question but the answer was not understood. >> I'm trying to work with the file 1PPB.pdb. There are 2 chains >> connected with a disulfide bond. Gromacs automatically adds H atoms. >> Although the disulfide bond is there, Gromacs ignore it because *each >> cystein is on a different chain*. So it adds H and therefor the >> disulfide bond is ruined during energy minimization. >> Is there any way to recreate such a disulfide bond (Please don't tell >> me again about "-ss" it works only on one chain. Moreover, the bond is >> existed on the pdf file.) or never ruined it at the first place? > > Yes, and the clue to how to combine the chains to give the mechanism a > chance of working is on the page I linked last time: > http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds > > Mark > -- next part ---------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120502/9c7e1646/attachment-0001.html > > -- > > Message: 3 > Date: Wed, 02 May 2012 09:12:13 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] Number of coordinate in topol.top and > solv.gro notmatching > T
[gmx-users] Number of coordinate in topol.top and solv.gro not matching
Hello all
I have to do MD simulation of ligand bound membrane protein in lipid bilayer.
Thus I am doing tutorialfor Protein - Ligand tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
I have used following command:
pdb2gmx -f 3HTB_clean.pdb -o conf.gro -water spc
editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
I am getting stuck at last command. Its showing following error:
Fatal error:
number of coordinates in coordinate file (solv.gro, 33049)
does not match topology (topol.top, 33064)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
{But when I calculate number of atom in topol.top and solv.gro it is same}
When I checked above http: I got that such type of error may be due to cpp
variable is not properly set in the .mdp file.
But When I locate ccp in my system and add it to .mdp file.
"
; LINES STARTING WITH ';' ARE COMMENTS
title = Minimization ; Title of run
cpp =/usr/bin/cpp
; Parameters describing what to do, when to stop and what to save
"
Then also it showing same error.
Please help me to solve this problem.
I am using gromacs-4.5.5 and installed with fftw-3.3.1 .
With regards
Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH
__
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202
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[gmx-users] Fatal error: Bond atom type names can't be single digits
Hello all I am new for gromacs. I have to do MD simulation of membrane protein docked with organic molecule. I have gerated top and itp for ligand using PRODRG server also generated top file for complex. But when I am generating .tpr file for a POPC system using grompp getting an error: creating statusfile for 1 node... checking input for internal consistency... calling /lib/cpp... processing topology... Cleaning up temporary file gromppWQnjOb Fatal error: Bond atom type names can't be single digits. I am using gromacs-4.5.5 Can someone help me to find out where is actually problem is occuring? With regards Sangita Kachhap SRF BIC,IMTECH CHANDIGARH __ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
