From: Ayşe Özlem Sezerman (asezerman_at_su.sabanciuniv.edu)
Date: Thu Mar 08 2007 - 00:11:00 CST
Thanks for your reply. But I could not understand how to proceed. I
would like to lear whether the reference coordinate file should be
different from the coordinate file in the config file.And what is the
importance of the reference coordinate file that we use in defining
Stern, Julie wrote:
>It looks like the prmtop,inpcrd, original pdb, and pdb from savePdb within leap all
>put the pdb files in different locations. So, I had to use ambpdb applying to the
>prmtop, inpcrd, to get an aligned pdb structure.
>The syntax is:
>ambpdb -p name.prmtop < name.inpcrd > new.pdb
>That pdb is aligned with the prmtop inpcrd, but if anyone knows a better way or a
>different way to use leap to align this, please post.
>From: Ayse Özlem Sezerman [mailto:asezerman_at_su.sabanciuniv.edu]
>Sent: Mon 3/5/2007 10:00 AM
>To: JC Gumbart
>Cc: Stern, Julie; namd-l_at_ks.uiuc.edu
>Subject: Re: namd-l: restraining parts of a molecule
>I am having the same problem at the moment. My reference coordinate file
>has the same coordinates as the one that is loaded. Maybe I missed it,
>but what should the reference coordinate file contain? Also in my force
>constant file I wrote the force constant values to column B for the
>atoms that are restrained. But I have seen no change when I changed the
>force constant values.
>JC Gumbart wrote:
>>I think it's more a question of if res.pdb has the same (or similar)
>>coordinates to whatever coordinates you are loading (either the pdb
>>or restart.coor file). The restrained_res.pdb is only used in this
>>case to read the force constant, NOT for coordinates.
>>My guess would be the coordinate file you're loading and the
>>coordinates in the restraint file are significantly different.
>>On Mar 4, 2007, at 10:20 PM, Stern, Julie wrote:
>>> I'm having some problems with applying a harmonic force
>>>constant to restrain parts
>>>of a protein. I tried a force constant of 5 and one of .5 and it
>>>has the same effect. It
>>>blows half the molecule right out of the water shell as a result of
>>>the minimization step,
>>>keeping a really long bond between the two parts of the molecule and
>>>an empty space
>>>where that part of the molecule was.
>>>Here is the code excerpt:
>>>Does anyone have any suggestions of what the force constant should
>>>be or what
>>>else I can check? Any ideas on why this might be happening? I
>>>doubled checked that the
>>>res.pdb and restrained_res.pdb have the same coordinates to start
>>>with so nothing is
>>>offset to begin with.
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