[gmx-users] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
Justin Lemkul
jalemkul at vt.edu
Fri Aug 12 14:15:28 CEST 2016
On 8/12/16 8:11 AM, Andreas Mecklenfeld wrote:
> Hello Mark,
>
> sorry for the confusion I've created. My system refers to a solute in water
> (which has only LJ-parameters for the oxygen atom). Within the solute, there are
> two approaches to deal with LJ-interactions:
>
> 1) intramolecular interactions (including 1-4 and far-off interactions)
> 2) intermolecular interactions with the oxygens of ambient water
>
> There are certain atom types, which handle points 1) and 2) with different sets
> of LJ-parameters. Since the water oxygen is not included within the solute
> topology, the pair potential between the affected solute atomtype and the
> water-oxygen atomtype therefore has to be intermolecular.
>
> My .top file looks like this:
>
> #########################################################################################################
>
>
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 2 yes 0.5 0.8333
>
> [ atomtypes ]
> ;name bond_type mass charge ptype sigma epsilon Amb
> o3 o3 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66
> 0.2100
> oa oa 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72
> 0.2104
> od od 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66
> 0.2100
> nd nd 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82
> 0.1700
> nl nl 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82
> 0.1700
> sh sh 0.00000 0.00000 A 3.56359e-01 1.04600e+00 ; 2.00
> 0.2500
> o3i o3i 0.00000 0.00000 A 0.331503 0.878640 ; 1.66 0.2100
> oai oai 0.00000 0.00000 A 0.295778 0.880314 ; 1.72 0.2104
> odi odi 0.00000 0.00000 A 0.320724 0.878640 ; 1.66 0.2100
> ndi ndi 0.00000 0.00000 A 0.349232 0.711280 ; 1.82 0.1700
> nli nli 0.00000 0.00000 A 0.299003 0.711280 ; 1.82 0.1700
> shi shi 0.00000 0.00000 A 0.334978 1.046000 ; 2.00 0.2500
> c3 c3 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91
> 0.1094
> hc hc 0.00000 0.00000 A 2.64953e-01 6.56888e-02 ; 1.49
> 0.0157
> c c 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91
> 0.0860
> o o 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66
> 0.2100
> n n 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82
> 0.1700
> hn hn 0.00000 0.00000 A 1.06908e-01 6.56888e-02 ; 0.60
> 0.0157
> cc cc 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91
> 0.0860
> cd cd 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91
> 0.0860
> h4 h4 0.00000 0.00000 A 2.51055e-01 6.27600e-02 ; 1.41
> 0.0150
> h5 h5 0.00000 0.00000 A 2.42146e-01 6.27600e-02 ; 1.36
> 0.0150
> na na 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82
> 0.1700
> h1 h1 0.00000 0.00000 A 2.47135e-01 6.56888e-02 ; 1.39
> 0.0157
> ss ss 0.00000 0.00000 A 3.56359e-01 1.04600e+00 ; 2.00
> 0.2500
> ca ca 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91
> 0.0860
> ha ha 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46
> 0.0150
> oh oh 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72
> 0.2104
> ho ho 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00
> 0.0000
> HW_tip4pew 1 1.008 0.0000 A 0.00000e+00 0.00000e+00
> OW_tip4pew 8 16.00 0.0000 A 3.16435e-01 6.80946e-01
> MW 0 0.0000 0.0000 D 0.00000e+00 0.00000e+00
>
> [ nonbond_params ]
> OW_tip4pew o3i 2 0.323969 0.773503
> OW_tip4pew oai 2 0.306107 0.774239
> OW_tip4pew odi 2 0.318579 0.773503
> OW_tip4pew ndi 2 0.332834 0.695948
> OW_tip4pew nli 2 0.307719 0.695948
> OW_tip4pew shi 2 0.325706 0.843961
>
>
>
> #include "Asn.itp"
> #include "tip4pew.itp"
>
>
>
> [ system ]
> Asn in tip4pew
>
>
> [ molecules ]
> ; molecule name nr.
> Asn 1
> SOL 900
>
>
>
> #########################################################################################################
>
>
> When I comment out the [ non_bond_params ] section, everything works fine, thus
> I would locate the error to this point.
> The error I receive is actually the one from the mail subject:
>
> ERROR 1 [file topol.top, line 44]:
> Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
>
> followed by repetitions regarding the other lines in the [ non_bond_params ]
> section.
>
You have specified type 2 for the [ nonbond_params ] section, which corresponds
to Buckingham. If you want normal LJ, set the type field to 1.
-Justin
>
>
> Thanks for your help!
> Andreas
>
>
>
>
>
> Am 12.08.2016 um 09:49 schrieb Mark Abraham:
>> Hi,
>>
>> On Fri, Aug 12, 2016 at 9:16 AM Andreas Mecklenfeld <
>> a.mecklenfeld at tu-braunschweig.de> wrote:
>>
>>> Hello Mark,
>>>
>>> thanks for the reply. The point is, I don't.
>>
>> Ah, I read your original email more closely now. The use of a subject line
>> that reflected your error message rather than your intention confused me.
>>
>>
>>> I found some Lennard-Jones
>>> parametrization in literature that distinguishes between intra- and
>>> intermolecular (oxygen atom of water) interactions.
>>
>> Um, typical water models have no intra-molecular LJ interactions.
>>
>>
>>> My intention was
>>> thus to define the specific eps_ij and sigma_ij for the corresponding
>>> atomtypes, which I thought should be dealt with in the [ nonbond_params
>>> ] section. All parameters are for Lennard-Jones and this is the
>>> potential I want to use. I have no idea why the usage of Buckingham is
>>> assumed. I'm using Gromacs 5.1 btw.
>>>
>> Then somewhere (e.g. [nonbond_params]) you are using a number that is being
>> interpreted as a function type that is Buckingham, which of course makes no
>> sense for a code that assumes each atom type has at most one set of LJ
>> parameters. But we haven't seen your full topology or full error message.
>>
>> Mark
>>
>>
>>> Thanks,
>>> Andreas
>>>
>>>
>>>
>>> Am 11.08.2016 um 17:59 schrieb Mark Abraham:
>>>> Hi,
>>>>
>>>> How do you want your atoms with lj parameters to interact with atoms with
>>>> Buckingham parameters?
>>>>
>>>> Mark
>>>>
>>>> On Fri, 5 Aug 2016 08:53 Andreas Mecklenfeld <
>>>> a.mecklenfeld at tu-braunschweig.de> wrote:
>>>>
>>>>> Dear Gromacs-users,
>>>>>
>>>>> I'm trying to modify some intermolecular Lennard-Jones interactions
>>>>> based on the GAFF force field. I've altered the topology file according
>>> to
>>>>>
>>>>>
>>> ############################################################################
>>>>> [ defaults ]
>>>>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>>>>> 1 2 yes 0.5 0.8333
>>>>>
>>>>> [ atomtypes ]
>>>>> ...
>>>>>
>>>>> [ nonbond_params ]
>>>>> type1 type2 sigma epsilon
>>>>> ...
>>>>>
>>>>> #include ...
>>>>>
>>>>> [ system ]
>>>>> ...
>>>>>
>>>>> [ molecules ]
>>>>> ...
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>> ############################################################################
>>>>> Sigma and epsilon for atoms type1 and type2 are calculated according to
>>>>> the Lorentz-Berthelot combination rule. The error I receive is
>>>>>
>>>>> "Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)",
>>>>> though I obviously want to use LJ and did not intentionally set any flag
>>>>> for Buckingham. Is there any way to fix this?
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Andreas
>>>>>
>>>>>
>>>>> --
>>>>> M. Sc. Andreas Mecklenfeld
>>>>> Stipendiat
>>>>>
>>>>> Technische Universität Braunschweig
>>>>> Institut für Thermodynamik
>>>>> Hans-Sommer-Straße 5
>>>>> 38106 Braunschweig
>>>>> Deutschland / Germany
>>>>>
>>>>> Tel: +49 (0)531 391-2634
>>>>> Fax: +49 (0)531 391-7814
>>>>>
>>>>> http://www.ift-bs.de
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
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>>>>> send a mail to gmx-users-request at gromacs.org.
>>> --
>>> M. Sc. Andreas Mecklenfeld
>>> Stipendiat
>>>
>>> Technische Universität Braunschweig
>>> Institut für Thermodynamik
>>> Hans-Sommer-Straße 5
>>> 38106 Braunschweig
>>> Deutschland / Germany
>>>
>>> Tel: +49 (0)531 391-2634
>>> Fax: +49 (0)531 391-7814
>>>
>>> http://www.ift-bs.de
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
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>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
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>>> send a mail to gmx-users-request at gromacs.org.
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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