[gmx-users] Re: Help with Gromacs
Tsjerk Wassenaar
tsjerkw at gmail.com
Wed Dec 23 22:39:41 CET 2009
Hi Pavan,
Please, I'm not a user list. This is in no way attached to the
tutorials of mine.
But your problem arises because you're mixing things up. You're using
a new run input (.tpr) file, and a checkpoint (.cpt) file. Either you
continue runs using checkpoint files (preferred) or you generate a new
.tpr file and use that, leaving the checkpoint file. This could for
instance be done because you want to change the output frequency for
some block.
The .part***. addition is added because you don't give the option
-append, that would otherwise cause the subsequent trajectory/energy
stuff be appended to already existing files. Without that option,
gromacs adds a part identifier to avoid overwriting existing files.
Cheers,
Tsjerk
On Wed, Dec 23, 2009 at 10:14 PM, Pavan Ghatty <pavanghatty at gmail.com> wrote:
> Restarts are still a cause of heart-burn Tsjerk.
> I have these files at the moment:
> 1ea5.grompp4.cpt
> 1ea5.grompp4.edr
> 1ea5.grompp4.gro
> 1ea5.grompp4.log
> 1ea5.grompp4.tpr
> 1ea5.grompp4.trr
> md.mdp --> http://compbio.ornl.gov/~pkc/md.txt
> The aim for now is to generate a bunch of 5ps trajectory files that look
> like 1ea5.grompp[4-100].trr .I will then use trjcat to concatenate all the
> .trr files. From my understanding mdrun needs .tpr (only topology is read)
> and .cpt files to extend a simulation.
>
> tpbconv -s ./1ea5.grompp4.tpr -f ./1ea5.grompp4.trr -e ./1ea5.grompp4.edr -o
> ./1ea5.grompp5.tpr
>
> This gave ./1ea5.grompp5.tpr with
> nsteps = 5000
> and such.
>
> Then,
> mdrun -v -s ./1ea5.grompp5.tpr -cpi ./1ea5.grompp4.cpt -deffnm
> ./1ea5.grompp5
> gave me,
> 1ea5.grompp5.tpr
> 1ea5.grompp5.part0002.xtc
> 1ea5.grompp5.part0002.trr
> 1ea5.grompp5.part0002.log
> 1ea5.grompp5.part0002.gro
> 1ea5.grompp5.part0002.edr
> 1ea5.grompp5.cpt
>
> I don't understand why the output of xtc/trr/log is not
> 1ea5.grompp5.(xtc/trr/log). This creates a problem with the next script
> which looks like:
> tpbconv -s ./1ea5.grompp5.tpr -f ./1ea5.grompp5.trr -e ./1ea5.grompp5.edr -o
> ./1ea5.grompp6.tpr -extend 5
> and so on. Just to see what happens I did
> tpbconv -s 1ea5.grompp5.tpr -f ./1ea5.grompp5.part002.trr -e
> ./1ea5.grompp5.part0002.edr -o ./1ea5.grompp6.tpr -extend 5
> and ran
> mdrun -v -s ./1ea5.grompp6.tpr -cpi ./1ea5.grompp5.cpt -deffnm
> ./1ea5.grompp6
>
> This gave
> 1ea5.grompp6.part0003.xtc
> 1ea5.grompp6.part0003.trr
> 1ea5.grompp6.part0003.log
> 1ea5.grompp6.part0003.gro
> 1ea5.grompp6.part0003.edr
>
> What am I doing wrong?
> g_energy -f 1ea5.grompp5.part0002.edr -o temp.xvg [total energy] gave
> 2.000000
> -834920.625000
> 3.000000 -831025.187500
> 4.000000 -829585.187500
> 5.000000 -828792.437500
> g_energy -f 1ea5.grompp6.part0003.edr -o temp.xvg [total energy] gave
> 5.000000 -828792.500000
> 6.000000 -828115.000000
> 7.000000 -828224.312500
> 8.000000 -827586.187500
> 9.000000 -828065.500000
> 10.000000 -828509.125000
> Since the energies at step 5.000 are (almost) the same from grompp5.trr and
> grompp6.trr, can I assume that the simulation is reliably moving forward?
> The trajectories at this time are too small to notice any jumps.
>
> Pavan
>
> On Tue, Dec 22, 2009 at 9:05 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>>
>> Hi Pavan,
>>
>> The first thing is to formulate your research question. Second you
>> have to determine which tools are best suited to investigate and
>> answer that question. Third, you have to determine how to use these
>> tools optimally to answer the question.
>> In your study you also have to consider how others have addressed the
>> same or similar issues previously and reflect on the correctness of
>> their approach.
>> That is about as specific as I can answer your question, as you
>> haven't given a formulation of your question. Aside from that, note
>> that your best option is likely to consist of several approaches
>> combined, and reflect on commonalities and differences between these.
>> In your case that would come down to performing simulations with both
>> 43a1/43a2 and 45a3. That will allow you to put the results from the
>> earlier study in scope.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Mon, Dec 21, 2009 at 3:56 PM, Pavan Ghatty <pavanghatty at gmail.com>
>> wrote:
>> > Sorry I hit the send button by mistake.
>> >>
>> >> Hi Tsjerk,
>> >> I managed to run the simulation over the weekend. But the question of
>> >> forcefield kept bothering me. Especially the attached paper. The aim of
>> >> my
>> >> simulation is to see the flexibility of the aromatic residues (chi_1
>> >> chi_2)
>> >> of 1ea5 in water at 300K. Page 12 of the paper attached is particularly
>> >> worrisome. An earlier paper on the topic titled "Flexibility of
>> >> aromatic
>> >> residues in the active-site gorge of Acetylcholinesterase: X-ray vs
>> >> molecular dynamics" published in 2008 used 43a1 ff. For the purposes of
>> >> this
>> >> simulation does it really matter which ff I use? I wrote to authors of
>> >> that
>> >> paper and I was simply referred to the Gromacs manual for information.
>> >> Now I
>> >> am completely confused.
>> >
>> > Thanks,
>> > Pavan
>> >
>> >
>> >>
>> >> On Wed, Dec 16, 2009 at 1:06 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
>> >> wrote:
>> >>>
>> >>> Hi Pavan,
>> >>>
>> >>> For me, the easy way out is this: The GROMOS FFs are parameterized
>> >>> with, and thus to be used with, SPC type solvent. The conditions used
>> >>> to derive a force field are in a sense part of that force field. Using
>> >>> TIP* solvent models with GROMOS is basically mixing force fields,
>> >>> which is considered bad practice.
>> >>>
>> >>> Cheers,
>> >>>
>> >>> Tsjerk
>> >>>
>> >>> On Wed, Dec 16, 2009 at 5:54 PM, Pavan Ghatty <pavanghatty at gmail.com>
>> >>> wrote:
>> >>> > Hi Tsjerk,
>> >>> > I managed to solvate the protein in tip3p water. to addions I need a
>> >>> > .trp
>> >>> > file which comes from grompp. Now grompp with minim.mdp file from
>> >>> > http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ dies with this
>> >>> > error
>> >>> > "atomtype OWT3 not found".
>> >>> > http://www.mail-archive.com/gmx-users@gromacs.org/msg15722.html has
>> >>> > some
>> >>> > info on it but I cannot figure out how to resolve it. The ff I am
>> >>> > using
>> >>> > ff45a3nb.itp does not have OWT3 atomtype in it. But the file
>> >>> > tip3p.itp
>> >>> > does
>> >>> > have OWT3 atomtype. The message grompp printed out are at
>> >>> > http://compbio.ornl.gov/~pkc/error. You can see in the file that the
>> >>> > program
>> >>> > does read the file tip3p.itp.
>> >>> > How do I make grompp recognize TIP3P water and OWT3 atomtype?
>> >>> > Thanks and sorry for bugging you. I'll keep it short.
>> >>> > Pavan
>> >>> >
>> >>> >
>> >>> > On Tue, Dec 15, 2009 at 11:19 AM, Tsjerk Wassenaar
>> >>> > <tsjerkw at gmail.com>
>> >>> > wrote:
>> >>> >>
>> >>> >> Hi Pavan,
>> >>> >>
>> >>> >> You can make local copies of such files in the working directory,
>> >>> >> which will get precedence over the global ones.
>> >>> >>
>> >>> >> Cheers,
>> >>> >>
>> >>> >> Tsjerk
>> >>> >>
>> >>> >> On Tue, Dec 15, 2009 at 4:49 PM, Pavan Ghatty
>> >>> >> <pavanghatty at gmail.com>
>> >>> >> wrote:
>> >>> >> > Hi Tsjerk,
>> >>> >> > I used AMBER to get the structure, then used VMD to strip the
>> >>> >> > hydrogens.
>> >>> >> > Now
>> >>> >> > pdb2gmx gave me a .gro and .top file but seems to have detected a
>> >>> >> > total
>> >>> >> > negative charge of 7 while AMBER and CHARMM (using
>> >>> >> > NAMD/VMD/CHARMM27
>> >>> >> > ff)
>> >>> >> > both detected -9. I am wondering how to overcome this problem.
>> >>> >> > There
>> >>> >> > is
>> >>> >> > also
>> >>> >> > a problem with disulphide bonds. I did use the -merge option with
>> >>> >> > pdb2gmx
>> >>> >> > but the Cysteine sulphurs have hydrogens anyway in the .gro
>> >>> >> >
>> >>> >> >
>> >>> >> > file. http://www.gromacs.org/Documentation/File_Formats/specbond.dat has
>> >>> >> > some information on how to deal with the issue but the
>> >>> >> > specbond.dat
>> >>> >> > file
>> >>> >> > seems to be in /usr/local/gromacs...location which is accessible
>> >>> >> > only by
>> >>> >> > root and here in the lab (oh btw I am a post-doc in Oak Ridge
>> >>> >> > National
>> >>> >> > Laboratory) very few people are given root access. Is there a way
>> >>> >> > to
>> >>> >> > make
>> >>> >> > pdb2gmx read specbond.dat file?
>> >>> >> > Thanks!
>> >>> >> > On Tue, Dec 15, 2009 at 10:19 AM, Tsjerk Wassenaar
>> >>> >> > <tsjerkw at gmail.com>
>> >>> >> > wrote:
>> >>> >> >>
>> >>> >> >> Hi Pavan,
>> >>> >> >>
>> >>> >> >> With AMBER you probably added all hydrogens, which would make
>> >>> >> >> pdb2gmx
>> >>> >> >> complain about hydrogen atoms that are not listed in the
>> >>> >> >> building
>> >>> >> >> blocks for the GROMOS FFs, which are united atom FFs. If that is
>> >>> >> >> the
>> >>> >> >> case, you can add -ignh on the command line to have Gromacs
>> >>> >> >> strip
>> >>> >> >> off
>> >>> >> >> all hydrogens present and rebuild only those needed according to
>> >>> >> >> the
>> >>> >> >> force field.
>> >>> >> >>
>> >>> >> >> Cheers,
>> >>> >> >>
>> >>> >> >> Tsjerk
>> >>> >> >>
>> >>> >> >> On Tue, Dec 15, 2009 at 4:11 PM, Pavan Ghatty
>> >>> >> >> <pavanghatty at gmail.com>
>> >>> >> >> wrote:
>> >>> >> >> > Hi Tsjerk,
>> >>> >> >> > Thanks for the reply. I used AMBER to get the proper structure
>> >>> >> >> > and
>> >>> >> >> > pdb2gmx still fails. I will try a few more times and if it
>> >>> >> >> > still
>> >>> >> >> > fails
>> >>> >> >> > I'll drop a line to gmx-users list.
>> >>> >> >> > Cheers!
>> >>> >> >> >
>> >>> >> >> > On 12/14/09, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>> >>> >> >> >> Hi Pavan,
>> >>> >> >> >>
>> >>> >> >> >> At the beginning of the tutorial you have to check whether
>> >>> >> >> >> your
>> >>> >> >> >> structure is missing residues and/or side chain atoms. The
>> >>> >> >> >> error
>> >>> >> >> >> message from pdb2gmx indicates that side chain atoms are
>> >>> >> >> >> missing.
>> >>> >> >> >> You
>> >>> >> >> >> will have to build these in some way first.
>> >>> >> >> >>
>> >>> >> >> >> By the way, it's not the Gromacs FF. It's GROMOS96, from the
>> >>> >> >> >> Van
>> >>> >> >> >> Gunsteren group in Zurich. Gromacs doesn't really have a
>> >>> >> >> >> force
>> >>> >> >> >> field
>> >>> >> >> >> of its own. For what it's worth, I'd also stick with the
>> >>> >> >> >> Gromos
>> >>> >> >> >> 45a3
>> >>> >> >> >> force field, rather than taking 53a6. My experiences with the
>> >>> >> >> >> latter
>> >>> >> >> >> are not very good.
>> >>> >> >> >>
>> >>> >> >> >> As a final note, it is better to post questions like these to
>> >>> >> >> >> the
>> >>> >> >> >> gmx-users list. I'm on there, but so are many more. That will
>> >>> >> >> >> ensure
>> >>> >> >> >> that you receive answers quicker and probably better.
>> >>> >> >> >>
>> >>> >> >> >> Best,
>> >>> >> >> >>
>> >>> >> >> >> Tsjerk
>> >>> >> >> >>
>> >>> >> >> >>
>> >>> >> >> >> On Mon, Dec 14, 2009 at 5:13 PM, Pavan Ghatty
>> >>> >> >> >> <pavanghatty at gmail.com>
>> >>> >> >> >> wrote:
>> >>> >> >> >>> Hello Tsjerk,
>> >>> >> >> >>>
>> >>> >> >> >>> I need a small favor with preparing a simulation box with
>> >>> >> >> >>> protein
>> >>> >> >> >>> (1ea5
>> >>> >> >> >>> has
>> >>> >> >> >>> a net negative charge of 9) in a box of water with 9 sodium
>> >>> >> >> >>> ions. I
>> >>> >> >> >>> am
>> >>> >> >> >>> using
>> >>> >> >> >>> your tutorial at
>> >>> >> >> >>> http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/
>> >>> >> >> >>> as
>> >>> >> >> >>> a
>> >>> >> >> >>> reference.
>> >>> >> >> >>>
>> >>> >> >> >>> I got 1ea5.pdb from PDB and used the following set of
>> >>> >> >> >>> commands.
>> >>> >> >> >>> mv 1ea5.pdb 1ea5.pdb.org
>> >>> >> >> >>> grep -v NAG 1ea5.pdb.org > 1ea5.pdb
>> >>> >> >> >>> pdb2gmx -f 1ea5.pdb -o 1ea5.gro -p 1ea5.top -water tip3p
>> >>> >> >> >>> Selected ff53a6.
>> >>> >> >> >>> Error/output:
>> >>> >> >> >>>
>> >>> >> >> >>> 1. It correctly identified the three disulphide bonds I am
>> >>> >> >> >>> interested
>> >>> >> >> >>> it
>> >>> >> >> >>> CYS64 CYS91 CYS228 CYS251 CYS262
>> >>> >> >> >>> CYS399
>> >>> >> >> >>> SG489 SG709 SG1757 SG1934 SG2022
>> >>> >> >> >>> SG3103
>> >>> >> >> >>> CYS91 SG709 !0.204!
>> >>> >> >> >>> CYS262 SG2022 2.226 2.157 3.288 !0.203!
>> >>> >> >> >>> CYS518 SG4098 3.269 3.463 1.117 4.102 4.286
>> >>> >> >> >>> !0.205!
>> >>> >> >> >>>
>> >>> >> >> >>> 2. Making bonds...
>> >>> >> >> >>> Opening library file
>> >>> >> >> >>> /share/build/gromacs-4.0.5/share/top/aminoacids.dat
>> >>> >> >> >>>
>> >>> >> >> >>> WARNING: atom CE is missing in residue LYSH 11 in the pdb
>> >>> >> >> >>> file
>> >>> >> >> >>> WARNING: atom NZ is missing in residue LYSH 11 in the pdb
>> >>> >> >> >>> file
>> >>> >> >> >>> WARNING: atom HZ1 is missing in residue LYSH 11 in the pdb
>> >>> >> >> >>> file
>> >>> >> >> >>> You might need to add atom HZ1 to the hydrogen
>> >>> >> >> >>> database of
>> >>> >> >> >>> residue
>> >>> >> >> >>> LYSH
>> >>> >> >> >>> in the file ff???.hdb (see the manual)
>> >>> >> >> >>> WARNING: atom CG is missing in residue ASN 39 in the pdb
>> >>> >> >> >>> file
>> >>> >> >> >>> WARNING: atom HD22 is missing in residue ASN 39 in the pdb
>> >>> >> >> >>> file
>> >>> >> >> >>> You might need to add atom HD22 to the hydrogen
>> >>> >> >> >>> database
>> >>> >> >> >>> of
>> >>> >> >> >>> residue
>> >>> >> >> >>> ASN
>> >>> >> >> >>> in the file ff???.hdb (see the manual)
>> >>> >> >> >>>
>> >>> >> >> >>> 3. After 44 such warnings it dies with this error:
>> >>> >> >> >>> -------------------------------------------------------
>> >>> >> >> >>> Program pdb2gmx, VERSION 4.0.5
>> >>> >> >> >>> Source code file: pdb2top.c, line: 704
>> >>> >> >> >>>
>> >>> >> >> >>> Fatal error:
>> >>> >> >> >>> There were 44 missing atoms in molecule Protein_A, if you
>> >>> >> >> >>> want
>> >>> >> >> >>> to
>> >>> >> >> >>> use
>> >>> >> >> >>> this
>> >>> >> >> >>> incomplete topology anyhow,
>> >>> >> >> >>> use the option -missing
>> >>> >> >> >>> -------------------------------------------------------
>> >>> >> >> >>>
>> >>> >> >> >>> Could you please help in understand where I am going wrong?
>> >>> >> >> >>> I
>> >>> >> >> >>> am
>> >>> >> >> >>> more
>> >>> >> >> >>> used
>> >>> >> >> >>> to running simulations in Amber and NAMD but I am currently
>> >>> >> >> >>> in
>> >>> >> >> >>> a
>> >>> >> >> >>> rather
>> >>> >> >> >>> tight situation where my boss wanted to test a simulation
>> >>> >> >> >>> with
>> >>> >> >> >>> Gromacs
>> >>> >> >> >>> ff.
>> >>> >> >> >>> I
>> >>> >> >> >>> know NAMD can run on Gromacs ff but I will still need
>> >>> >> >> >>> Gromacs
>> >>> >> >> >>> inputs
>> >>> >> >> >>> for
>> >>> >> >> >>> that
>> >>> >> >> >>> [http://www.ks.uiuc.edu/Research/namd/2.7b2/ug/node15.html].
>> >>> >> >> >>> Any
>> >>> >> >> >>> help
>> >>> >> >> >>> will be greatly appreciiated.
>> >>> >> >> >>> Thanks!
>> >>> >> >> >>>
>> >>> >> >> >>> --
>> >>> >> >> >>> Pavan K. Ghatty
>> >>> >> >> >>>
>> >>> >> >> >>>
>> >>> >> >> >>
>> >>> >> >> >>
>> >>> >> >> >>
>> >>> >> >> >> --
>> >>> >> >> >> Tsjerk A. Wassenaar, Ph.D.
>> >>> >> >> >>
>> >>> >> >> >> Computational Chemist
>> >>> >> >> >> Medicinal Chemist
>> >>> >> >> >> Neuropharmacologist
>> >>> >> >> >>
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >> > --
>> >>> >> >> > Pavan K. Ghatty
>> >>> >> >> >
>> >>> >> >>
>> >>> >> >>
>> >>> >> >>
>> >>> >> >> --
>> >>> >> >> Tsjerk A. Wassenaar, Ph.D.
>> >>> >> >>
>> >>> >> >> Computational Chemist
>> >>> >> >> Medicinal Chemist
>> >>> >> >> Neuropharmacologist
>> >>> >> >
>> >>> >> >
>> >>> >> >
>> >>> >> > --
>> >>> >> > Pavan K. Ghatty
>> >>> >> >
>> >>> >> >
>> >>> >>
>> >>> >>
>> >>> >>
>> >>> >> --
>> >>> >> Tsjerk A. Wassenaar, Ph.D.
>> >>> >>
>> >>> >> Computational Chemist
>> >>> >> Medicinal Chemist
>> >>> >> Neuropharmacologist
>> >>> >
>> >>> >
>> >>> >
>> >>> > --
>> >>> > Pavan K. Ghatty
>> >>> >
>> >>> >
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> Tsjerk A. Wassenaar, Ph.D.
>> >>>
>> >>> Computational Chemist
>> >>> Medicinal Chemist
>> >>> Neuropharmacologist
>> >>
>> >>
>> >>
>> >> --
>> >> Pavan K. Ghatty
>> >>
>> >
>> >
>> >
>> > --
>> > Pavan K. Ghatty
>> >
>> >
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> Computational Chemist
>> Medicinal Chemist
>> Neuropharmacologist
>
>
>
> --
> Pavan K. Ghatty
>
>
--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
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