Re: amber-developers: ptraj

From: Thomas Cheatham III <>
Date: Thu, 3 Jan 2008 13:24:19 -0700 (Mountain Standard Time)

> Is there an (implicit) assumption in ptraj that the "POINTERS" block
> immediately follows the "TITLE" block in prmtop? Also, is the "TITLE" block
> limited to one line? Of course, it makes perfect sense to do so (reminds me
> the old days Peter used to put very long titles on his papers :) ). But, is
> it easy to remove these assumptions/limits? I occasionally like to add a few
> lines to remind me exactly what I did when I play around. I can potentially
> add a "NOTE" block. But, that would be illegal, isn't it?

The prmtop is extensible, so there is nothing illegal about adding a note

ptraj does at present assume that %VERSION, %FLAG, %POINTERS go in that
order and first, but after that the order does not matter. Moreover,
ptraj mistakenly does not use the flags but assumes the order which is
technically not correct...

The reason your prmtop files work with sander is that it ignores these
extra lines of text. In the short term, I will make ptraj compatible with
your modification and sander. I have done this in my amber10 version but
do not have the appropriate karma (permissions) to update ptraj in the
amber10 tree at scripps.

Longer term we may think about common specifications in the prmtop file,
such as force fields, keywords, and user supplied information, but in the
meantime, your hack should be OK.


p.s. DAC, maybe you can open the permissions to src/ptraj in amber10 on
Received on Sat Jan 05 2008 - 00:03:32 PST
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