[gmx-users] pdb2gmx -water-> grompp; grompp error
Paymon Pirzadeh
ppirzade at ucalgary.ca
Tue Aug 25 23:12:07 CEST 2009
I realized sth about the previous error message I posted. In the
following I have copied the lines (with their line number) which
grompp gives warning on!
in .gro file:
65868 10940SOL HW265866 5.038 5.739 6.407
65869 10940SOL MW65867 5.103 5.710 6.455
65870 10940SOL LP165868 5.061 5.644 6.524
65871 10940SOL LP265869 5.144 5.630 6.405
65872 10941Na Na65870 1.844 0.957 1.889
65873 5.40000 6.23500 10.24600
in .top file:
4147 [ molecules ]
4148 ; Compound #mols
4149 Protein_A 1
4150 SOL 10903
4151 Na+ 1
I have tested that if I remove the "+" sign, grompp will not work at all
and says "such molecule does not exists".
So, I am not sure where the Na-NA mismatch comes from?!
Payman
On Tue, 2009-08-25 at 15:59 -0400, Justin A. Lemkul wrote:
>
> Paymon Pirzadeh wrote:
> > When I look at the .top file generated by pdb2gmx, the last lines show
> > how this -0.99 is generated:
> >
> > 442 opls_302 37 ARG CZ 138 0.64 12.011 ;
> > qtot -0.33
> > 443 opls_300 37 ARG NH1 139 -0.8 14.0067 ;
> > qtot -1.13
> > 444 opls_301 37 ARG HH11 139 0.46 1.008 ;
> > qtot -0.67
> > 445 opls_301 37 ARG HH12 139 0.46 1.008 ;
> > qtot -0.21
> > 446 opls_300 37 ARG NH2 140 -0.8 14.0067 ;
> > qtot -1.01
> > 447 opls_301 37 ARG HH21 140 0.46 1.008 ;
> > qtot -0.55
> > 448 opls_301 37 ARG HH22 140 0.46 1.008 ;
> > qtot -0.09
> > 449 opls_271 37 ARG C 141 0.7 12.011 ;
> > qtot 0.61
> > 450 opls_272 37 ARG O1 141 -0.8 15.9994 ;
> > qtot -0.19
> > 451 opls_272 37 ARG O2 141 -0.8 15.9994 ;
> > qtot -0.99
> >
> > The charged side-chains are Arg, Lys, 2 * Asp and Glu. Since the pH of
> > simulation is supposed to be close to 7.0, I believe one of the
> > negatively-charged side chains needs to be neutralized. That's why I
> > think one Na+ might be helpful.
> >
>
> That's probably correct. I just wanted to verify what was in your system. If
> you just had water, it made no sense. But with a protein involved with lots of
> partial charges, these rounding issues do occur. You really do have a system
> with -1 charge.
>
> -Justin
>
> > Payman
> >
> >
> > On Tue, 2009-08-25 at 15:45 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> OK! It worked! Thanks a lot again. But I have a final technical
> >>> question. After running grompp, it shows that my box has a net charge of
> >>> -0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is
> >>> OK?! or even this 0.01 charge will cause me troubles?
> >> Depending on the size of your system, rounding errors can occur. It is unusual
> >> that the hundredths place would be showing this error. Usually you'd get
> >> something like 0.99998 or something. Your water topology has a zero net charge;
> >> is there something else in your system causing the -1 charge?
> >>
> >> Adding a single Na+ to neutralize the charge may be appropriate, but that's up
> >> to you based on what's in your system (something else may be broken, but I just
> >> don't know).
> >>
> >> -Justin
> >>
> >>> Sorry for tons of e-mails.
> >>> regards,
> >>>
> >>> Payman
> >>>
> >>>
> >>> On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote:
> >>>> Paymon Pirzadeh wrote:
> >>>>> OK! That's fine. But what if I do not have permissions to make such
> >>>>> changes in the itp files? Also, isn't that the case that when you define
> >>>> That's why I said copy the force field files into your local directory. Once
> >>>> there, you can modify them.
> >>>>
> >>>>> sth for the second time, grompp will take the second one? Sorry for mass
> >>>>> of e-mail!
> >>>>>
> >>>> That is only true in the case of .mdp files.
> >>>>
> >>>> -Justin
> >>>>
> >>>>> Payman
> >>>>>
> >>>>>
> >>>>>
> >>>>> On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote:
> >>>>>> Paymon Pirzadeh wrote:
> >>>>>>> I have done that already! I use my local copy to make my files. but how
> >>>>>>> can I get rid of this error? get into the oplsaanb.itp or include this
> >>>>>>> water model in the topology file before oplsaa.itp?
> >>>>>>>
> >>>>>> I don't understand what you're saying you've already done.
> >>>>>>
> >>>>>> The problem is this: when grompp attempts to assemble the .tpr file, it reads
> >>>>>> all of the information from the ffoplsaa*.itp files. It finds the directives
> >>>>>> like [defaults], [atomtypes], etc in a pre-defined order. If, later, it finds a
> >>>>>> duplicate of these directives, it complains. So when you #include your .itp
> >>>>>> file with new [atomtypes], it generates the error because it is a duplicate
> >>>>>> directive. You have to include the new atom types in ffoplsaanb.itp in the
> >>>>>> [atomtypes] directive of this file. The rest of the topology shouldn't cause a
> >>>>>> problem, just the [atomtypes] directive.
> >>>>>>
> >>>>>> -Justin
> >>>>>>
> >>>>>>> Payman
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> On Tue, 2009-08-25 at 14:14 -0400, Justin A. Lemkul wrote:
> >>>>>>>> Paymon Pirzadeh wrote:
> >>>>>>>>> OK!
> >>>>>>>>> here is the .itp file which I generated. I might upload it because it
> >>>>>>>>> has passed the initial tests.
> >>>>>>>>>
> >>>>>>>>> ; This is an itp file to describe water's six-site model by H. Nada and
> >>>>>>>>> J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413
> >>>>>>>>> (2003)
> >>>>>>>>> ; This model is a combination of TIP4P and TIP5P. It has three LJ sites
> >>>>>>>>> and 3 Coulomb sites
> >>>>>>>>> ; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
> >>>>>>>>> 111.00 degrees, O-M and O-L are about 0.230A and 0.8892A respectively
> >>>>>>>>>
> >>>>>>>>> [ defaults ]
> >>>>>>>>> ; non-bondedtype combrule genpairs FudgeLJ
> >>>>>>>>> FudgeQQ N
> >>>>>>>>> 1 2 NO
> >>>>>>>>>
> >>>>>>>>> [ atomtypes ]
> >>>>>>>>> ;name mass charge ptype c6 c12
> >>>>>>>>> OW 15.9994 0.0 A 0.3115 0.714845562
> >>>>>>>>> HW 1.00800 0.477 A 0.0673 0.11541
> >>>>>>>>> MW 0.000 -0.866 D 0.00 0.00
> >>>>>>>>> LW 0.00 -0.044 D 0.00 0.00
> >>>>>>>>>
> >>>>>>>>> [ moleculetype ]
> >>>>>>>>> ;molname nrexcl
> >>>>>>>>> SOL 2
> >>>>>>>>>
> >>>>>>>>> [ atoms ]
> >>>>>>>>> ; nr atomtype resnr residuename atom cgnr charge
> >>>>>>>>> 1 OW 1 SOL OW 1 0.0
> >>>>>>>>> 2 HW 1 SOL HW1 1 0.477
> >>>>>>>>> 3 HW 1 SOL HW2 1 0.477
> >>>>>>>>> 4 MW 1 SOL MW 1 -0.866
> >>>>>>>>> 5 LW 1 SOL LP1 1 -0.044
> >>>>>>>>> 6 LW 1 SOL LP2 1 -0.044
> >>>>>>>>>
> >>>>>>>>> [ settles ]
> >>>>>>>>> ; OW function doh dhh
> >>>>>>>>> 1 1 0.0980 0.15856
> >>>>>>>>>
> >>>>>>>>> [ dummies3 ]
> >>>>>>>>> ; These set of parameters are for M site which can be easily calculated
> >>>>>>>>> using TIP4P calculations from tip4p.itp
> >>>>>>>>> ; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
> >>>>>>>>> b*(r(i)-r(k))
> >>>>>>>>> ; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
> >>>>>>>>> Remember that OM is in the same direction of OH bonds.
> >>>>>>>>> ; Remember this site is in the same plane of OH bonds; so, its function
> >>>>>>>>> 1
> >>>>>>>>> ;
> >>>>>>>>> ; site from function a b
> >>>>>>>>> 4 1 2 3 1 0.199642536 0.199642536
> >>>>>>>>>
> >>>>>>>>> ; Now we define the position of L sites which can be obtained from
> >>>>>>>>> tip5p.itp
> >>>>>>>>> ; So, it will be described as dummy site 3out: r(v) = r(i) +
> >>>>>>>>> a*(r(i)-r(j)) + b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
> >>>>>>>>> ; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
> >>>>>>>>> |a|=|b|=const/2. since the lone pairs are in opposite direction of OH
> >>>>>>>>> bonds, a minus sign is added. This part is similar to M site.
> >>>>>>>>> ; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
> >>>>>>>>> the magnitude of vector product of OH bonds.
> >>>>>>>>> ; This sites are tetrahedral sites; so, its function 4
> >>>>>>>>> ;
> >>>>>>>>> ; site from function a b
> >>>>>>>>> c
> >>>>>>>>> 5 1 2 3 4 -0.437172388 -0.437172388
> >>>>>>>>> 8.022961206
> >>>>>>>>> 6 1 2 3 4 -0.437172388 -0.437172388
> >>>>>>>>> -8.022961206
> >>>>>>>>>
> >>>>>>>>> [ exclusions ]
> >>>>>>>>> 1 2 3 4 5 6
> >>>>>>>>> 2 1 3 4 5 6
> >>>>>>>>> 3 1 2 4 5 6
> >>>>>>>>> 4 1 2 3 5 6
> >>>>>>>>> 5 1 2 3 4 6
> >>>>>>>>> 6 1 2 3 4 5
> >>>>>>>>>
> >>>>>>>>> and here is the message I get from grompp:
> >>>>>>>>>
> >>>>>>>>> Program grompp_d_mpi, VERSION 4.0.5
> >>>>>>>>> Source code file: topio.c, line: 415
> >>>>>>>>>
> >>>>>>>>> Fatal error:
> >>>>>>>>> Syntax error - File sixsitewater.itp, line 12
> >>>>>>>>> Last line read:
> >>>>>>>>> '[ atomtypes ]'
> >>>>>>>>> Invalid order for directive atomtypes
> >>>>>>>>> -------------------------------------------------------
> >>>>>>>>>
> >>>>>>>>> I believe the original files of GROMACS need admin permissions which I
> >>>>>>>>> do not have on the cluster that I am currently using and I am not sure
> >>>>>>>>> if that might not cause troubles for other users. So, I thought how I
> >>>>>>>>> can keep the changes local.
> >>>>>>>>>
> >>>>>>>> Make a copy in your local directory; grompp will use these before looking for
> >>>>>>>> system-wide files. As a general rule, whenever developing new parameters or
> >>>>>>>> adjusting files, do so locally before potentially messing yourself (or others) up :)
> >>>>>>>>
> >>>>>>>> -Justin
> >>>>>>>>
> >>>>>>>>> Payman
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> On Tue, 2009-08-25 at 13:53 -0400, Justin A. Lemkul wrote:
> >>>>>>>>>> Paymon Pirzadeh wrote:
> >>>>>>>>>>> Hello,
> >>>>>>>>>>> Just a reminder that I had troubled with combination rules between my
> >>>>>>>>>>> water model and GROMACS forcefields. I fixed the problem by adjusting my
> >>>>>>>>>>> water model's parameters. BUT, now, I specified the new parameters in
> >>>>>>>>>>> my .itp file under [ atomtype ] category and grompp makes errors out of
> >>>>>>>>>>> the orders. Now I am using OPLSaa. I suspect again the problem comes
> >>>>>>>>>>> from the presence of the second [atomtype ]. How can I keep my new
> >>>>>>>>>>> parameters and use them in my water model's itp file? Or should I change
> >>>>>>>>>>> these parameters in the OPLSaa.itp file?
> >>>>>>>>>> You can't have a second [atomtypes] directive. You can add new parameters to
> >>>>>>>>>> ffoplsaanb.itp to account for the atom types you are implementing, though.
> >>>>>>>>>>
> >>>>>>>>>> If you want anything more specific, you'll probably have to provide the topology
> >>>>>>>>>> file you're working with, as well as any actual error messages you're seeing.
> >>>>>>>>>>
> >>>>>>>>>> -Justin
> >>>>>>>>>>
> >>>>>>>>>>> Regards,
> >>>>>>>>>>>
> >>>>>>>>>>> Payman
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>> On Wed, 2009-08-19 at 10:20 +1000, Mark Abraham wrote:
> >>>>>>>>>>>> Paymon Pirzadeh wrote:
> >>>>>>>>>>>>> I checked all the force-fields available in the GROAMCS. None of them
> >>>>>>>>>>>>> have the #2 combination rule which matches my water model! Any
> >>>>>>>>>>>>> alternatives (rather than changing my water model)?
> >>>>>>>>>>>> A water model that isn't compatible with the model of the solutes isn't
> >>>>>>>>>>>> of any value, so it looks like you have put the cart before the horse.
> >>>>>>>>>>>>
> >>>>>>>>>>>> Mark
> >>>>>>>>>>>>
> >>>>>>>>>>>>> On Tue, 2009-08-18 at 18:52 -0400, Justin A. Lemkul wrote:
> >>>>>>>>>>>>>> Paymon Pirzadeh wrote:
> >>>>>>>>>>>>>>> That was very helpful! But I realized a problem. The OPLSaa uses the
> >>>>>>>>>>>>>>> combination rule #3 in [ defaults ] while my water model uses #2. Now if
> >>>>>>>>>>>>>>> I comment out my water model's combination, I am not sure what I am
> >>>>>>>>>>>>>>> going to face! Any comments?
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Then I would say that your water model's combination rule is inconsistent with
> >>>>>>>>>>>>>> the method of nonbonded calculations in OPLS. It appears that the only
> >>>>>>>>>>>>>> difference between combination rules 2 and 3 comes when a specific interaction
> >>>>>>>>>>>>>> is not defined in the [nonbond_params] section. The specifics of these
> >>>>>>>>>>>>>> combination rules are given in manual section 5.3.3.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> -Justin
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Payman
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> On Tue, 2009-08-18 at 18:19 -0400, Justin A. Lemkul wrote:
> >>>>>>>>>>>>>>>> Paymon Pirzadeh wrote:
> >>>>>>>>>>>>>>>>> Well,
> >>>>>>>>>>>>>>>>> I changed the topology file of the system and manually typed the .itp of
> >>>>>>>>>>>>>>>>> my own water model. Just a reminder that I have used my own water
> >>>>>>>>>>>>>>>>> model's .itp file successfully in pure water systems. This .itp file
> >>>>>>>>>>>>>>>>> starts from [ defaults ] and contains all information needed. But when
> >>>>>>>>>>>>>>>>> it comes to grompp, the following error appears:
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> Program grompp_d_mpi, VERSION 4.0.5
> >>>>>>>>>>>>>>>>> Source code file: topio.c, line: 415
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> Fatal error:
> >>>>>>>>>>>>>>>>> Syntax error - File sixsitewater.itp, line 6
> >>>>>>>>>>>>>>>>> Last line read:
> >>>>>>>>>>>>>>>>> '[ defaults ]'
> >>>>>>>>>>>>>>>>> Invalid order for directive defaults
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> The only time that [defaults] should appear is in the force field that you are
> >>>>>>>>>>>>>>>> calling (i.e., ffoplsaa.itp):
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> http://oldwiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> -Justin
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> I am trying to use this water model with OPLSaa. what kind of directive
> >>>>>>>>>>>>>>>>> am I missing?
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> Payman
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> On Tue, 2009-08-18 at 16:05 -0400, Justin A. Lemkul wrote:
> >>>>>>>>>>>>>>>>>> Paymon Pirzadeh wrote:
> >>>>>>>>>>>>>>>>>>> Hello,
> >>>>>>>>>>>>>>>>>>> I am trying to use a different water model for my proteins (using oplsaa
> >>>>>>>>>>>>>>>>>>> force field). I use the .itp file which I developed, but pdb2gmx does
> >>>>>>>>>>>>>>>>>>> not accept it. I am a bit confused on how I can make my water model work
> >>>>>>>>>>>>>>>>>>> with OPLSaa. Based on what I saw from spc.itp or other samples, do I
> >>>>>>>>>>>>>>>>>>> need to change the names of my particles in my water .itp file by
> >>>>>>>>>>>>>>>>>>> including _FF_OPLS?
> >>>>>>>>>>>>>>>>>> I don't know how pdb2gmx decides how to recognize water models; it may be
> >>>>>>>>>>>>>>>>>> hard-coded. In any case, your atom types have to be consistent with OPLS
> >>>>>>>>>>>>>>>>>> standards; as for whether or not you need the #ifdef _FF_OPLS in your .itp file,
> >>>>>>>>>>>>>>>>>> you may not need it if OPLS is the only force field with which it will be used.
> >>>>>>>>>>>>>>>>>> The #ifdef blocks just prevent a GROMOS system from trying to recognize OPLS, etc.
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>> -Justin
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>> Regards,
> >>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>> Payman
> >>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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> >>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>> _______________________________________________
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> >>>>>>>>>>>>>
> >>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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> >>>>>>>>>>>>
> >>>>>>>>>>> _______________________________________________
> >>>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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> >>>>>>>>>>>
> >>>>>> --
> >>>>>> ========================================
> >>>>>>
> >>>>>> Justin A. Lemkul
> >>>>>> Ph.D. Candidate
> >>>>>> ICTAS Doctoral Scholar
> >>>>>> 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 mailing list gmx-users at gromacs.org
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> >>>>>>
> >>>>>>
> >>>
> >
> >
>
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