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

[Irem Altan]

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).

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

--
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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

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