[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] 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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Today's Topics:
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 jalem...@vt.edu
Subject: Re: [gmx-users] Question regarding genion
To: Discussion list for GROMACS users gmx-users@gromacs.org
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 jalem...@vt.edu
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 gmx-users@gromacs.org
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/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
[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 jalem...@vt.edu 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 gmx-users@gromacs.org 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.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
[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] 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 jalem...@vt.edu 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 gmx-users@gromacs.org 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 jalem...@vt.edu Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs To: Discussion list for GROMACS users gmx-users@gromacs.org 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 jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *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 and angles in a residue , or make dihedrals in a residue ( or with atoms in next ones) plus the charge of a the residue should be defined properly in .rtp files to define the new residue in aminoacid.rtp file of CHARMM36 force field. So I arranged this lines to define formyl in .rtp file. And I got the topology. But there are some questions for me here: 1. How can I be sure the formyl which I defined is correct? Is getting the topology is enough to be sure of the correct output? It is incorrect. As I said before, a formyl group is an aldehyde and has an H atom attached to C, e.g. -CH(=O). At present, you are defining a -C=O group with an incomplete carbon valence. http://en.wikipedia.org/wiki/Aldehyde
[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] 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 elto...@if.usp.br Subject: Re: [gmx-users] keep the nanotube cylindrical. To: Za Pour za.p...@yahoo.com, Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: caoyvbokmjs-te_r-6uxh+k8zmct83mmknjnuccazfzd+wpp...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 On Sat, May 5, 2012 at 7:27 PM, Za Pour za.p...@yahoo.com 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 francesco.ot...@gmail.com Subject: [gmx-users] poor performance in Hemiltonian Replica Exchange To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAFQcp-PpW0prmq=uuMCAJcOoEgQYwbP1=berej-insh_af4...@mail.gmail.com 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/attachments/20120510/f5452d69/attachment-0001.html -- Message: 3 Date: Thu, 10 May 2012 14:20:44 -0400 From: Michael Shirts mrshi...@gmail.com Subject: Re: [gmx-users] poor performance in Hemiltonian Replica Exchange To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CA+zJb
[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] 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 jalem...@vt.edu Subject: Re: [gmx-users] How to remove H atom from residue in gro file? To: Discussion list for GROMACS users gmx-users@gromacs.org 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 mark.abra...@anu.edu.au Subject: Re: [gmx-users] How to remove H atom from residue in gro file? To: Discussion list for GROMACS users gmx-users@gromacs.org 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 jalem...@vt.edu Subject: Re: [gmx-users] Number of coordinate in topol.top and solv.gro notmatching To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4fa132ad.1060...@vt.edu Content-Type: text/plain; charset=UTF-8; format=flowed On 5/2/12 8:14 AM, Sangita Kachhap wrote: 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
[gmx-users] Nubmer of coordinate not matching in topol.top and sol.gro
.)
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
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Message: 5
Date: Wed, 02 May 2012 13:43:18 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Number of cooredinate in topol.top and
solv.gro notmatching
To: Discussion list for GROMACS users gmx-users@gromacs.org
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 reply
When I am appending ligand from .gro file and generating complex the new .gro
file newbox.gro do not have ligand.
Command I have used: editconf -f conf.gro -o newbox.gro -bt dodecahedron -d
1.0
I am appending ligand like this at the end of conf.gro
163ASN HD21 1689 1.029 -0.671 -0.401
163ASN HD22 1690 0.944 -0.584 -0.525
163ASN C 1691 0.621 -0.740 -0.126
163ASN O1 1692 0.624 -0.616 -0.140
163ASN O2 1693 0.683 -0.703 -0.011
1JZ4 C4 1 2.429 -2.412 -0.007
1JZ4 C14 2 2.392 -2.470 -0.139
1JZ4 C13 3 2.246 -2.441 -0.181
1JZ4 C12 4 2.229 -2.519 -0.308
1JZ4 C11 5 2.169 -2.646 -0.295
1JZ4 H11 6 2.135 -2.683 -0.199
1JZ4 C7 7 2.155 -2.721 -0.411
1JZ4 H7 8 2.104 -2.817 -0.407
1JZ4 C8 9 2.207 -2.675 -0.533
1JZ4 H8 10 2.199 -2.738 -0.621
1JZ4 C9 11 2.267 -2.551 -0.545
1JZ4 H9 12 2.306 -2.516 -0.640
1JZ4 C10 13 2.277 -2.473 -0.430
1JZ4 OAB 14 2.341 -2.354 -0.434
1JZ4 HAB 15 2.369 -2.334 -0.528
5.99500 5.19182 9.66100 0.0 0.0 -2.99750 0.0
0.0
0.0
Have you correctly incremented the second line of conf.gro to indicate that
more
atoms have been added? Without it, editconf will read the wrong number of
lines
and exclude the ligand.
Thanks for reply.
I have changed line number in conf.gro and now its working.
-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
[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
