Re: [AMBER] problem in writing pdb with ambpdb

From: David A Case <>
Date: Mon, 19 Dec 2011 08:20:38 -0500

On Mon, Dec 19, 2011, Jio M wrote:
> I am using prep file and created prmtop file and inpcrd. Job runs
> smoothly. Now when I wanted to save pdb using ambpdb the atom names in
> pdb are not printed correctly. My prep file has many atoms having four
> letters (like C218), which are obviously printed in prmtop file also.
> but while writing pdb file from prmtop file and restart file ambpdb gets
> confused. But TOP2MOL2 works fine.
> e.g. here are prmtop some lines:
> %FORMAT(20a4)
> C218H18RH18SH18TC217H17RH17SC216H16RH16SC215H15RH15SC214H14RH14SC213H13RH13SC212
> H12RH12SC211H11RH11SC210H101C29 H91 C28 H8R H8S C27 H7R H7S C26 H6R H6S C25 H5R
> H5S C24 H4R H4S C23 H3R H3S C22 H2R H2S C21 O22 O21 C2  C1  O11 P   O13 O14 O12
> Actually names are C218 H18R H18S H18S and so on...
> but pdb (from ambpdb) write names as RH18 SH18, but top2mol2 is working OK.

Sounds like you may have an older version of ambpdb(?). What version are you

For pdb format version 2, which was used up until a couple of years ago, the
atom symbol had to be in the 2nd column(!) of the atom name. The only way to
handle a four-letter name was to "wrap" the final letter to the beginning.

But this has changed in pdb format version 3, which is what current ambpdb
files should be using. Now four character names will be left-justified, as
you expect.

If you are using up-to-date code, please try to construct a small example
that illustrates the problem.


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Received on Mon Dec 19 2011 - 05:30:08 PST
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