[gmx-users] renumber ligand atom numbers

[Justin Lemkul]

On 2/27/16 7:52 AM, Sana Saeed wrote:
> yes i used 2023 in the index file also. my distance restraints are one protein
> atom (atm num 120) and ligand atom 2023)  but the error is about 2023, that it
> is out of range. may be the order of directive is incorrect.
> first i #include forcefield
> 2nd #include ligand topology
> 3rd protein topology contents
> 4th distance restraints
> 5th angle restraints
> 6th dihedral restraints
> 7th position restrain protein
>

Yes, this is wrong, because you're essentially defining the restraint as only 
part of the protein and grompp interprets those atoms as being local to the 
protein only.  The [intermolecular_interactions] must be defined in the .top, 
after [molecules].  Only then is the full, global system established.

...

[ system ]
protein complex

[ molecules ]
protein 1
lig     1
(whatever)

[intermolecular_interactions]
[distance_restraints]
...
(whatever else)

Note that in the case of a simple distance restraint, the pull code is much 
easier.  Dihedrals, angles, etc. are really powerful with 
[intermolecular_interactions] and those are the cases you usually need to use it.

-Justin

>
> Sana Saeed Khan,
> Teaching-Research Assistant
> Chemoinformatics Lab
> Graduate Student, MS bioinfo
> Department of Bioinformatics
> Soongsil University, Seoul, South Korea.
>
>
> On Saturday, February 27, 2016 5:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> Please keep the discussion on the mailing list.
>
> On 2/27/16 7:34 AM, Sana Saeed wrote:
>  > (Sorry i mentioned atom number 1 in first reply)
>  > i want to apply distance restrain on the ligand atom number 3, but this atom
>  > number also exist in protein?? so is it okay to specify atom number3 or should i
>  > use the numbering of that atom from gro file, because its different (atom number
>  > 2023) in gro file and index file from topology file. which numbering should i
>  > consider.
>
> If this is in relation to your [intermolecular_interactions] then the numbers
> specified there are the global atom numbers *from the coordinate file* and have
> no relation to the individual topologies.  So atom 3 is unambiguously defined as
> that of the protein, and you must use 2023.
>
> -Justin
>
>  > Sana Saeed Khan,
>  > Teaching-Research Assistant
>  > Chemoinformatics Lab
>  > Graduate Student, MS bioinfo
>  > Department of Bioinformatics
>  > Soongsil University, Seoul, South Korea.
>  >
>  >
>  > On Saturday, February 27, 2016 5:14 PM, Justin Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>  >
>  >
>  >
>  >
>  > On 2/27/16 6:04 AM, Sana Saeed wrote:
>  >  > hii am performing protein ligand binding free energy calculation through
>  >  > alchemical pathway. i made both topologies and generated distance, dihedral
>  >  > and angle restraints. in the index file i defined the restrained atoms. the
>  >  > error i got in energy minimization grompp is that the atom is out of range.
>  >  > it is because my protein is starting from atom num 1 and also my ligand
>  >  > starts with 1. in the gro file the numbering is changed , protein starts with
>  >
>  > No, grompp is complaining because (I'm guessing, since you haven't provided us
>  > with an exact error message) you're specifying a completely nonexistent atom
>  > number somewhere.
>  >
>  >  > 1 and ends with 1020 , and ligand starts after 1020. but in topology i
>  >  > included the ligand.itp (from acpype) into complex topology file, and both
>  >  > molecules starts with 1. how can i change the numbering of ligand atoms as in
>  >
>  > Don't alter the topology numbering.  It is a different concept from number in a
>  > coordinate file.  All [moleculetype] definitions MUST start from 1.  If you
>  > alter it, grompp will fail for a different reason.  Sort out the grompp problem
>  > you have now, not the one you'll create by breaking your topology.
>  >
>  > -Justin
>  >
>  >
>  >  > gro file. pdb2gmx -renum is not working because it is small ligand not a
>  >  > protein or peptide. if there is any code or any program please suggest.
>  >  > thanks in advance. Sana Saeed Khan,Teaching-Research
>  >  > AssistantChemoinformatics LabGraduate Student, MS bioinfoDepartment of
>  >  > BioinformaticsSoongsil University, Seoul, South Korea.
>  >
>  >  >
>  >
>  > --
>  > ==================================================
>  >
>  > 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 <mailto:jalemkul at outerbanks.umaryland.edu>
> <mailto:jalemkul at outerbanks.umaryland.edu
> <mailto:jalemkul at outerbanks.umaryland.edu>> |
>  > (410) 706-7441
>  > http://mackerell.umaryland.edu/~jalemkul
>
>  >
>  >
>  > ==================================================
>  >
>  >
>
> --
> ==================================================
>
> 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 <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>

-- 
==================================================

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

==================================================