[gmx-users] mapping indices in posre/topol files to those in index files

[Justin Lemkul]

On 7/25/16 3:14 PM, Irem Altan wrote:
> I am trying to assign different force constants to different atoms. I also have a handful of atoms that I would like to freeze (specifically the atoms that drift away from their PDB positions).
>

And you need these custom restraints applied to all three of the identical chains?

The simplest thing to do is create one or more restraint .itp files with 
genrestr by providing it a coordinate file with *only* the first chain (using 
suitable index group(s) as needed, again only ever created from the first 
chain).  Since they're all identical, and numbering corresponds to topological 
numbering (i.e., always from 1), then the first chain can be used to represent 
any of them.

Create as many files as you need with different force constants (or just one, 
and edit its contents) and #include them however you need.

-Justin

> Best,
> Irem
>
> On Jul 25, 2016, at 3:06 PM, Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:
>
>
>
> On 7/25/16 3:03 PM, Irem Altan wrote:
> Hi,
>
> I have .pdb file that contains of three copies of a protein with two chains each. For convenience I had named both chains of each copy identically. I therefore have a .pdb file that looks like this:
>
> ATOM … A …
> ….
> ATOM … A …
> TER
> ATOM … A …
> ….
> ATOM … A …
> TER
> ATOM … B …
> ….
> ATOM … B …
> TER
> ATOM … B …
> ….
> ATOM … B …
> TER
> ATOM … C …
> ….
> ATOM … C …
> TER
> ATOM … C …
> ….
> ATOM … C …
> TER
>
> When I do pdb2gmx, this produces the following topol files:
>
> topol_Protein_chain_A.itp
> topol_Protein_chain_A2.itp
> topol_Protein_chain_B.itp
> topol_Protein_chain_B2.itp
> topol_Protein_chain_C.itp
> topol_Protein_chain_C2.itp
>
> (the posre_* files are named similarly).
>
> The indices of atoms in these files always start from 1. However, when I create an index file, the indices are such that all atoms are numbered from 1 to the total number of atoms in the system. Therefore atom #1 in a topol file maps to some other number in the index file. The question is, in what order the atoms are counted? After the last atom of chain_A, do I continue with the first atom of chain_A2, etc.?
>
>
> What are you trying to accomplish?  Position restraint numbering is based on [moleculetype] numbering.  Index groups are based on global atom numbering in the coordinate file.  There are different conventions because they are used for different things.
>
> -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<mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
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-- 
==================================================

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

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