[gmx-users] on atomtypes
brettliu123 at 163.com
Thu May 12 17:42:19 CEST 2016
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?
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 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
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