[gmx-users] pdb2gmx , or equivalent

[Justin Lemkul]

On 11/15/19 5:15 PM, Ling Chan wrote:
> I see, thank you Justin. Suppose you mean ASP vs ASH, HID, HIE, HIP, etc.?

Yes, as well as all the constituent hydrogen atoms.

> But how about disulfide bridges? Does pdb2gmx respect SSBOND and / or CONECT records in the PDB? Perhaps it will re-evaluate them regardless?

pdb2gmx automatically detects them based on S-S distances. If you want 
to override/change what pdb2gmx detects, you have to do that 
interactively. CONECT records are never used.

> Also, I see on the pdb2gmx manual page that the default glutamine is charged. What does it mean?

Glutamine is almost never charged and most force fields don't support 
it. There is a -gln option that allows you to define protonation state, 
but if pdb2gmx sees GLN it is the neutral form.

-Justin

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Justin A. Lemkul, Ph.D.
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