[gmx-users] grompp warning with ion's name
Paymon Pirzadeh
ppirzade at ucalgary.ca
Tue Aug 25 22:52:32 CEST 2009
After adding the Na ion, grompp gives the following error:
processing coordinates...
Warning: atom name 65870 in AFP_I.top and
AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)
WARNING 1 [file AFP_I.top, line 4151]:
1 non-matching atom name
atom names from AFP_I.top will be used
atom names from AFP_I_solvated_54_62_102_null.gro will be ignored
This is while I could not find such the mentioned mismatch in the two
files. Should I ignore this warning?
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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