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

[Qing Lv]

At 2017-06-23 21:55:39, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>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).



This is just what I have tried and succeeded eventually... Previously I made some mistakes when converting .top files to .itp.
Thanks.
Qing


>
>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.
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