[gmx-users] on atomtypes

[Brett]

Dear Justin,

You see, the ligand.itp contains the HS14 information as following,

....

  34    NT    1     ADP     N6    7   -0.859  14.0067
   35  HS14    1     ADP    H10    7    0.406   1.0080

   36  HS14    1     ADP    H11    7    0.419   1.0080
....


But when I run
gmx grompp -f ions.mdp -c target_solv.gro -p topol.top -o ions.tpr,

it told me the "Atomtype HS14 not found".

Will you please show me the way to have the issue settled?

Brett










At 2016-05-12 23:20:14, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>On 5/12/16 11:17 AM, Brett wrote:
>> Dear All,
>>
>> Following is the part of the atomtypes.atp  for gromos54a7:
>>
>>     O  15.99940 ;     carbonyl oxygen (C=O)
>>    OM  15.99940 ;     carboxyl oxygen (CO-)
>>    OA  15.99940 ;     hydroxyl, sugar or ester oxygen
>>    OE  15.99940 ;     ether or ester oxygen
>>    OW  15.99940 ;     water oxygen
>>     N  14.00670 ;     peptide nitrogen (N or NH)
>>    NT  14.00670 ;     terminal nitrogen (NH2)
>>    NL  14.00670 ;     terminal nitrogen (NH3)
>>    NR  14.00670 ;     aromatic nitrogen
>>    NZ  14.00670 ;     Arg NH (NH2)
>>    NE  14.00670 ;     Arg NE (NH)
>>     C  12.01100 ;     bare carbon
>>   CH0  12.0110  ;     bare sp3 carbon, 4 bound heavy atoms
>>   CH1  13.01900 ;     aliphatic or sugar CH-group
>>   CH2  14.02700 ;     aliphatic or sugar CH2-group
>>   CH3  15.03500 ;     aliphatic CH3-group
>>   CH4  16.04300 ;     methane
>>  CH2r  14.02700 ;     CH2-group in a ring
>>   .......
>>
>> If I need to insert a new type list for example HS14 with weight 1.0080, should the word description of the atomtype (for example, "CH2-group in a ring" for "CH2r  14.02700") should be accurate or just a kind of reminder which the gromacas will not read?
>>
>
>It's a comment; it's not used for anything.  Note that atomtypes.atp is only 
>read by pdb2gmx, so if this is related to your earlier post (and if it is, it's 
>better to continue a thread than to start a whole new topic) then you don't need 
>to be editing this file.  You need to be adding parameters in ffnonbonded.itp or 
>the ligand's .itp file itself.
>
>> In addition, the atomtypes.atp is a readonly file in /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/. WIll you please let me know how to save it after the HS14 atomtype was added?
>>
>
>Make a local copy of the directory, acquire admin privileges, or (most simply) 
>add missing parameters into the ligand's .itp file.
>
>-Justin
>
>-- 
>==================================================
>
>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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