[gmx-users] pdb2gmx: can we use a file to specify the protonation instead of using "-inter"?

Christopher Neale chris.neale at alum.utoronto.ca
Thu May 21 16:59:45 CEST 2015

Dear Cheng:

You can define protonation states like this:

echo "0 1 2" | pdb2gmx -ff amber99sb-ildn -water tip3p -his

That will give you, in order for three HIS residues:
0. H on ND1 only (HID)
1. H on NE2 only (HIE)
2. H on ND1 and NE2 (HIP)

You can also use -inter, but you'll need to do a dry-run to see what order gmx asks you for these things in. From my tests, it follow an order that is first residue type (in order: LYS, ARG, GLN, ASP, GLU, HIS, disulfide bonds) and for each of these, order by residue number.


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Zhang, Cheng <c.zhang.11 at ucl.ac.uk>
Sent: 21 May 2015 10:38
To: gromacs.org_gmx-users at maillist.sys.kth.se
Cc: Zhang, Cheng
Subject: [gmx-users] pdb2gmx: can we use a file to specify the protonation instead of using "-inter"?

Dear GROMACS experts,

Can I ask is there a more efficient way to deal with the "-inter" option in the pdb2gmx command?

Now, I have to manually assign individual protonation status one by one, which takes a very long time. Sometimes I make a mistake and I have to re-do all of them again.

Would it be possible if the command line can link to a file, which specifies the protonation for individual residues?

Thank you very much.

Yours sincerely

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