[gmx-users] Regarding parameters of octane box in ffamber99sb - ildn
YUVRAJ UBOVEJA
yuvrajthedon at gmail.com
Thu Dec 9 05:22:59 CET 2010
Hello all
I have to create an octane box for studying effect of solvent hydrophobicity
on enzyme activation.
Anyone using octane parameterized file in amber?
Please suggest me how to parameterize it or is there any tutorial for it.
As i am a beginner, so plz explain in steps.
Thanks a lot.
Yuvraj
On Mon, Dec 6, 2010 at 6:05 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: Constraining two virtual sites (Mark Abraham)
> 2. Re: Help - LINCS WARNING: bonds that rotated more than 30
> degrees (Justin A. Lemkul)
> 3. RE: Constraining two virtual sites (Berk Hess)
>
>
> ---------- Forwarded message ----------
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date: Mon, 06 Dec 2010 22:31:55 +1100
> Subject: Re: [gmx-users] Constraining two virtual sites
> On 6/12/2010 9:43 PM, Sebastian Fritsch wrote:
>
>> Hi everybody,
>>
>>
>> I have some trouble setting up topology for my, I admit, quite unusual
>> system. I need to constrain the center of masses of two groups of atoms to a
>> fixed 'bond' length. Since I have to do this for every molecule I cannot use
>> the 'pull constraint' of the free energy code.
>>
>> Thus in my topology I defined a com vsite for each group and tried to
>> apply a constraint between them. The atoms within each group are connected
>> by harmonic springs forming a ring polymer (for those of you who know it:
>> this is supposed to become the path integral representation in the end...)
>> The topol.top for a single molecule test system looks like this:
>>
>> [ defaults ]
>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>> 1 1 no 1.0 1.0
>> [ atomtypes ]
>> ;name mass charge ptype C6 C12 ; sigma
>> epsilon
>> A 1.00800 0 A 0 0
>> B 1.00800 0 A 0 0
>> C 1.00800 0 A 0 0
>> VS 0.000 0 V 0 0
>> [ moleculetype ]
>> ; molname nrexcl
>> SOL 0
>> [ atoms ]
>> ; id at resnr resnm atnm cgnr charge
>> 1 VS 1 A V1 1 0
>> 2 VS 1 B V2 2 0
>> 3 A 1 A A 3 0 4 B 1 A B
>> 4 0 5 C 1 A C 5 0 6 A 1 B
>> A 6 0 7 B 1 B B 7 0 8
>> C 1 B C 8 0 [ virtual_sitesN ]
>> ;
>> 1 2 3 4 5
>> 2 2 6 7 8
>> [ bonds ]
>> ; ai aj
>> 3 4 1 0 1687
>> 4 5 1 0 1687
>> 5 3 1 0 1687
>> 6 7 1 0 1687
>> 7 8 1 0 1687
>> 8 6 1 0 1687
>> [ constraints ]
>> ; ai aj funct length_A
>> 1 2 1 0.1633
>> [ system ]
>> TEST
>> [ molecules ]
>> SOL 1
>>
>> The conf.gro is setup such that the constraint is satisfied initially.
>>
>> When I run the simulation with LINCS the constraint seem to be not applied
>> at all, the distance beetween the two vsites increases just as in free
>> diffusion. With SHAKE the system explodes immediately (without error
>> message, but every value is inf or nan).
>> I am running the system with the sd integrator in (vers. 4.5.3) but also
>> tried md and no thermostat, with no change in results.
>>
>> I appreciate any advice on this!
>>
>> Thanks,
>> Sebastian
>>
>
> I can't see anything that looks wrong. Make sure you inspect the output of
> grompp thoroughly for clues about how it's interpreting the .top file. You
> may like to use gmxcheck to compare the .tpr files produced under various
> permutations to see that things look like they're working correctly
> (remember atom numbers will start from zero in the output). Try putting the
> virtual site atoms after the real atoms in the ordering.
>
> Mark
>
>
>
> ---------- Forwarded message ----------
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> To: YUVRAJ UBOVEJA <yuvraj.uboveja at students.iiit.ac.in>, "Gromacs Users'
> List" <gmx-users at gromacs.org>
> Date: Mon, 06 Dec 2010 07:31:08 -0500
> Subject: [gmx-users] Re: Help - LINCS WARNING: bonds that rotated more than
> 30 degrees
>
> Please keep all Gromacs-related correspondence on the gmx-users list. I am
> not a private help service. I am CC'ing the list and would ask that
> anything further be posted there.
>
> Before posting anything to the list, check the list archive. Your problem
> has been posted and answered literally thousands of times. Even better, the
> Gromacs site is full of helpful information, like the following:
>
> http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> -Justin
>
> YUVRAJ UBOVEJA wrote:
>
>> Hello Sir
>>
>> Good Morning
>>
>> I am working on 1CRL.pdb (lipase with open lid). It had NAG which was
>> removed from the pdb.
>> I am using gromacs 4.5.3. I am posting all my steps here and all necessary
>> .mdp files are attached.
>>
>> 1. pdb2gmx (forcefield used amber99sb-ildn with tip3p model)
>> 2) editconf -bt dodecahedron -f 1.gro -c -d 1.0
>>
>> 3) genbox -cp 1CRL_step2.pdb -cs tip4p.gro -o 1CRL_b4em.pdb -p topol.top
>>
>> 4) grompp -f em.mdp -c 1CRL_b4em.pdb -p 1CRL_top1.top -o 1CRL_em.tpr
>>
>> 5) genion -p -s 1CRL_em.tpr -o 1CRL_ion.pdb -pname NA+ -np 17 -g
>> 1CRL_ion.log
>> 6) grompp -f em.mdp -c 1CRL_ion.pdb -p topol.top -o 1CRL_em.tpr
>> 7) mdrun -s 1CRL_em.tpr -o 1CRL_em.trr -c 1CRL_b4pr.pdb -g em.log -e
>> em.edr
>>
>> 8) grompp -f pr.mdp -c 1CRL_b4pr.pdb -r 1CRL_b4pr.pdb -p topol.top -o
>> 1CRL_pr.tpr
>>
>> 9) mdrun -s 1CRL_pr.tpr -o 1CRL_pr.trr -c 1CRL_b4md.pdb -g pr.log -e
>> pr.edr
>>
>> It is giving Error as follows:
>> *
>> Step 7, time 0.014 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000039, max 0.000512 (between atoms 5125 and 5126)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5126 31.8 0.1010 0.1009 0.1010
>>
>> Step 8, time 0.016 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000018, max 0.000869 (between atoms 5125 and 5126)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5126 33.9 0.1009 0.1011 0.1010
>>
>> Step 32, time 0.064 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000035, max 0.001516 (between atoms 5125 and 5127)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5127 34.2 0.1010 0.1008 0.1010
>>
>> Step 33, time 0.066 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000041, max 0.001609 (between atoms 5125 and 5126)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5127 32.7 0.1008 0.1009 0.1010
>>
>> Step 39, time 0.078 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000038, max 0.001576 (between atoms 5125 and 5126)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5127 34.5 0.1010 0.1011 0.1010
>>
>> Step 40, time 0.08 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000049, max 0.002593 (between atoms 5125 and 5127)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5127 34.3 0.1011 0.1013 0.1010
>>
>> Step 41, time 0.082 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000025, max 0.000573 (between atoms 5125 and 5127)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5127 31.5 0.1013 0.1011 0.1010
>>
>> Step 42, time 0.084 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000037, max 0.001815 (between atoms 5125 and 5127)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5127 34.7 0.1011 0.1008 0.1010
>>
>> Step 43, time 0.086 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000033, max 0.001302 (between atoms 5125 and 5127)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5127 32.2 0.1008 0.1009 0.1010
>>
>> Step 51, time 0.102 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000036, max 0.001418 (between atoms 5125 and 5127)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5126 30.5 0.1012 0.1010 0.1010
>>
>> Step 55, time 0.11 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000048, max 0.002660 (between atoms 4571 and 4573)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 4571 4572 36.5 0.1010 0.1010 0.1010
>>
>> Step 56, time 0.112 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000042, max 0.002092 (between atoms 4571 and 4573)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 4571 4572 36.4 0.1010 0.1010 0.1010
>>
>> Step 57, time 0.114 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000028, max 0.000763 (between atoms 4571 and 4573)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 4571 4572 31.8 0.1010 0.1010 0.1010
>>
>> Step 63, time 0.126 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000027, max 0.000427 (between atoms 4571 and 4572)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 4571 4573 32.7 0.1011 0.1010 0.1010
>>
>> Step 64, time 0.128 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000068, max 0.003175 (between atoms 5125 and 5126)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>>
>> Step 64, time 0.128 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000040, max 0.001591 (between atoms 4571 and 4573)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5127 35.2 0.1010 0.1012 0.1010
>> 4571 4573 37.2 0.1010 0.1008 0.1010
>>
>> Step 65, time 0.13 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000049, max 0.002173 (between atoms 5125 and 5126)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>>
>> Step 65, time 0.13 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000027, max 0.000553 (between atoms 4571 and 4573)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5127 35.0 0.1012 0.1011 0.1010
>> 4571 4573 31.0 0.1008 0.1009 0.1010
>>
>> Step 66, time 0.132 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000038, max 0.001188 (between atoms 5125 and 5127)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5127 35.6 0.1011 0.1009 0.1010
>>
>> Step 67, time 0.134 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000050, max 0.002202 (between atoms 5125 and 5126)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5127 31.4 0.1009 0.1009 0.1010
>>
>> Step 71, time 0.142 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000041, max 0.001740 (between atoms 5125 and 5126)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5126 34.6 0.1010 0.1012 0.1010
>>
>> Step 72, time 0.144 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000033, max 0.000836 (between atoms 5125 and 5127)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5126 34.2 0.1012 0.1011 0.1010
>>
>> Step 73, time 0.146 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000040, max 0.001326 (between atoms 5125 and 5126)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5126 38.5 0.1011 0.1009 0.1010
>>
>> Step 74, time 0.148 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000028, max 0.000900 (between atoms 5125 and 5127)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5126 32.6 0.1009 0.1010 0.1010
>> ^C
>>
>> Received the INT signal, stopping at the next NS step
>>
>>
>> Step 80, time 0.16 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000039, max 0.001703 (between atoms 5125 and 5126)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5126 30.8 0.1010 0.1012 0.1010
>>
>> Step 81, time 0.162 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000045, max 0.002178 (between atoms 5125 and 5126)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 5125 5126 30.8 0.1012 0.1012 0.101*0
>>
>>
>> Kindly give me a solution.
>>
>> Thanks
>>
>>
>> Yuvraj Uboveja
>> M. Tech Bioinformatics
>> CCNSB, IIIT-H
>>
>>
>> On Thu, Nov 18, 2010 at 5:25 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>> YUVRAJ UBOVEJA wrote:
>>
>> Dear Dr. Lemkul
>>
>> I was following your tutorial on lysozyme in water. In which you
>> have suggested to remove crystal water from the PDB file. As I
>> am an amateur in simulations, just started with GROMACS
>> Please find some time to answer my queries which could be very
>> silly in nature.
>>
>> Why do we want to delete crystal water?
>>
>>
>> I did this for ease of understanding. In previous Gromacs versions,
>> crystal waters and those added later showed up as separate "SOL"
>> blocks in the topology, which was not always easy to understand.
>>
>>
>> How do we come to know whether crystal water is required for our
>> simulation or not.
>>
>>
>> If these water molecules serve a functional role, do not remove
>> them. The paper that discusses the structure should have this
>> information. Most of the time, crystal waters are unimportant.
>>
>>
>> What is difference between crystal water already present in PDB
>> and water moleclues we add in solvation step. Is there any
>> functional difference wrt to simulation.
>>
>>
>> A crystal water comes from solvent conditions used during x-ray
>> diffraction. Anything else is added. Functional roles are
>> determined experimentally (see above comment).
>>
>>
>> One more thing how do we decide whether to use OPLS / AMBER
>> force field for our system (in my case it is lipase 1TRH). I got
>> to know that OPLS parameter have been created taking explicitly
>> solvent molecule in consideration. So in my view OPLS is more
>> better for solvating a protein for any solvent simulations.
>>
>>
>> I don't know how you came to this conclusions. Any of the force
>> fields provided in Gromacs are quite suitable to protein
>> simulations. They are all based on different quantum mechanical or
>> thermodynamic assumptions. You should spend some (significant) time
>> reading about each of the force fields and what they assume, and any
>> limitations they might have.
>>
>> -Justin
>>
>>
>> Thanks in anticipation.
>>
>> Best Regards
>>
>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/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
>
> ========================================
>
>
>
> ---------- Forwarded message ----------
> From: Berk Hess <gmx3 at hotmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date: Mon, 6 Dec 2010 13:34:35 +0100
> Subject: RE: [gmx-users] Constraining two virtual sites
> Hi,
>
> Unfortunately constraints can not be applied to virtual sites and grompp
> apparently
> does not not check for this. I will add a check.
> Constraints between virtual sites can lead to very complex constraint
> equations
> between the masses involved. Thus the general case if difficult to
> implement.
> Your cases seems quite simple and could be done with the pull code,
> if it would support more than one reference group, which I was thinking to
> implement.
>
> How many molecules do you have?
>
> Berk
>
> > Date: Mon, 6 Dec 2010 11:43:45 +0100
> > From: fritsch at mpip-mainz.mpg.de
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] Constraining two virtual sites
> >
> > Hi everybody,
> >
> >
> > I have some trouble setting up topology for my, I admit, quite unusual
> > system. I need to constrain the center of masses of two groups of atoms
> > to a fixed 'bond' length. Since I have to do this for every molecule I
> > cannot use the 'pull constraint' of the free energy code.
> >
> > Thus in my topology I defined a com vsite for each group and tried to
> > apply a constraint between them. The atoms within each group are
> > connected by harmonic springs forming a ring polymer (for those of you
> > who know it: this is supposed to become the path integral representation
> > in the end...)
> > The topol.top for a single molecule test system looks like this:
> >
> > [ defaults ]
> > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> > 1 1 no 1.0 1.0
> > [ atomtypes ]
> > ;name mass charge ptype C6 C12 ;
> > sigma epsilon
> > A 1.00800 0 A 0 0
> > B 1.00800 0 A 0 0
> > C 1.00800 0 A 0 0
> > VS 0.000 0 V 0 0
> > [ moleculetype ]
> > ; molname nrexcl
> > SOL 0
> > [ atoms ]
> > ; id at resnr resnm atnm cgnr charge
> > 1 VS 1 A V1 1 0
> > 2 VS 1 B V2 2 0
> > 3 A 1 A A 3 0
> > 4 B 1 A B 4 0
> > 5 C 1 A C 5 0
> > 6 A 1 B A 6 0
> > 7 B 1 B B 7 0
> > 8 C 1 B C 8 0
> > [ virtual_sitesN ]
> > ;
> > 1 2 3 4 5
> > 2 2 6 7 8
> > [ bonds ]
> > ; ai aj
> > 3 4 1 0 1687
> > 4 5 1 0 1687
> > 5 3 1 0 1687
> > 6 7 1 0 1687
> > 7 8 1 0 1687
> > 8 6 1 0 1687
> > [ constraints ]
> > ; ai aj funct length_A
> > 1 2 1 0.1633
> > [ system ]
> > TEST
> > [ molecules ]
> > SOL 1
> >
> > The conf.gro is setup such that the constraint is satisfied initially.
> >
> > When I run the simulation with LINCS the constraint seem to be not
> > applied at all, the distance beetween the two vsites increases just as
> > in free diffusion. With SHAKE the system explodes immediately (without
> > error message, but every value is inf or nan).
> > I am running the system with the sd integrator in (vers. 4.5.3) but also
> > tried md and no thermostat, with no change in results.
> >
> > I appreciate any advice on this!
> >
> > Thanks,
> > Sebastian
> >
> >
> >
> >
> >
> > --
> > gmx-users mailing list gmx-users at 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-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> --
> gmx-users mailing list
> gmx-users at 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!
>
--
Yuvraj Uboveja
M.Tech. Bioinformatics
IIIT Hyderabad
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