[gmx-users] pdb2gmx -water-> grompp; grompp error
Justin A. Lemkul
jalemkul at vt.edu
Tue Aug 25 21:59:57 CEST 2009
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
>>>>>>>>>>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>>>>>>>>>>>>>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> 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/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/mailing_lists/users.php
>>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> 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/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/mailing_lists/users.php
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> 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/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/mailing_lists/users.php
>>>>>>>>>>>
>>>>>> --
>>>>>> ========================================
>>>>>>
>>>>>> 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
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>>>>>>
>>>>>>
>>>
>
>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list