[gmx-users] confirm please

Justin Lemkul jalemkul at vt.edu
Tue May 13 01:50:12 CEST 2014

On 5/12/14, 7:32 PM, Chetan Mahajan wrote:
> Dear All,
> I am using amber2gromacs tool acpype for converting input files for AMBER
> into those for GROMACS. There are some differences in these files (.gro and
> .top) compared to the information given in gromacs manual 4.6.5 abotu these
> kind of files.
> First, while listing charges and vander waals parameters for all the atom
> types in [atomtypes] directive, there is no second column titled as
> "at.num" in the manual. Is that okay? What does that column mean anyways
> (number of atoms of that type?)?

Atomic number from the periodic table.  Not a necessary column.  The parsing 
code determines how many fields there are in the input and interprets them 

> Second, where there is atom name and number to be mentioned for each atom
> in a given molecule in .gro file,
> numbering is not consecutively for all atoms as mentioned in the manual.
> E.g. instead of OW1, HW1 and HW2 for water, it is just O, H1 and H2.
> Instead of O1, O2 in formate, it's just O, O1.

Naming conventions may differ by force field.  In this case, at worst it's a 
trivial mismatch that doesn't indicate any problem at all.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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