[gmx-users] 5-letter atom names in topology files

[Justin Lemkul]

On 6/23/17 9:53 AM, Qing Lv wrote:
> I tried pdb2gmx -merge interactive or -chainsep interactive, but neither work...

There is no chain information in a .gro so this approach cannot work.  If you 
have a multimeric complex, and you need to use these weird 5-character names, 
process each .gro separately and merge the topologies manually (convert .top -> 
.itp and list them as #include statements in a new .top).

Or:

1. Use a different force field that doesn't require format-breaking atom names.
2. Change the names in the .rtp and coordinate file to preserve format standards.

-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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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