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.
Chris.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Zhang, Cheng
c.zhang...@ucl.ac.uk
Sent: 21 May 2015 10:38
To: gromacs.org_gmx-users@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
Cheng
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