[gmx-users] RE: LJ-14 default.....

[Henrik Rundgren]

--__--__-- Message: 7 Subject: Re: [gmx-users] Help: No default LJ-14... 
From: David van der Spoel <spoel at xray.bmc.uu.se> To: 
gmx-users at gromacs.org Organization: Date: 20 Nov 2003 09:07:41 +0100 
Reply-To: gmx-users at gromacs.org On Thu, 2003-11-20 at 09:00, Henrik 
Rundgren wrote:

>> hello all.
>> I have a problem.
>> I have run some simulations with Gromacs, and all seems fine.
>> No I try to run a small peptide in wter, and I get the following warnings:
>> 
>>  Generated 1179 of the 1378 non-bonded parameter combinations
>> WARNING 1 [file "top.top", line 86]:
>>   No default LJ-14 types, using zeroes
>> WARNING 2 [file "top.top", line 87]:
>>   No default LJ-14 types, using zeroes
>> WARNING 3 [file "top.top", line 88]:
>>   No default LJ-14 types, using zeroes
>> WARNING 4 [file "top.top", line 109]:
>>   No default LJ-14 types, using zeroes
>> WARNING 5 [file "top.top", line 110]:
>>   No default LJ-14 types, using zeroes
>> WARNING 6 [file "top.top", line 111]:
>>   No default LJ-14 types, using zeroes
>> Excluding 3 bonded neighbours for Protein 1
>> Excluding 2 bonded neighbours for SOL 884
>> 
>> Then it continues and makes the infile .trp, but I doubt that this is ok 
>> to run an simulation on....
>> I have checked in the topology file, and the default type value is 1 
>> (=LJ)... so I don't see where this warning is coming from.
>> 
>have you checked which atom pair is listed in top.top lines 86, 87, 88,
>109-111
>
>  
>
>>> thanks for the help.
>>> sincerely,
>>> henrik
>>    
>>
> -- David. 
> ________________________________________________________________________ 
> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group, 
> Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, 
> Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 
> 755 spoel at xray.bmc.uu.se spoel at gromacs.org 
> http://xray.bmc.uu.se/~spoel 
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>


Hello,
Yes, I have looked in it.. but I can't understand why it would want to 
use the ZN: or SI: or NA:pairs in the topology file... since I haven't 
defined any "metals" in the pdb file (it's just a basic dipeptide of ALA 
ZW-form). 
I have missed some basics here... shouldn't the topology only include 
the atoms defined from the pdb file's?
(I used your spc216 file for water though. but that one seems ok when 
looking at it...)

 From top.top following can be read...

 [ nonbond_params ]
line   ; i j func c6 c12
86     O NL 1 0.23473E-02 0.34518E-05
87     O NR5* 1 0.23473E-02 0.20711E-05
88     O ZN 1 0.00000E+00 0.10931E-06
109   OM NR6* 1 0.23473E-02 0.33890E-05
110   OM SI 1 0.57734E-02 0.86722E-05
111   OM NA 1 0.40370E-03 0.44478E-06

thanks for input.
henrik

-- 
_________________________________________________________________
Henrik Rundgren
Division of Physical Chemistry
Arrhenius Laboratory
Stockholm University
S-106 91 Stockholm
Sweden

E-mail:    Henrik at physc.su.se
Telephone: +46-(0)8-16 12 63
Fax:       +46-(0)8-15 21 87
Website:   www.fos.su.se/~henrik
_________________________________________________________________

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