RE: restraining parts of a molecule

From: Stern, Julie (
Date: Mon Mar 05 2007 - 13:33:08 CST

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 zlem Sezerman []
Sent: Mon 3/5/2007 10:00 AM
To: JC Gumbart
Cc: Stern, Julie;
Subject: Re: namd-l: restraining parts of a molecule

Hi ,
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.

constraints on
consKCol B
consRef ./coordref.pdb
consKFile ./restrain.pdb


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:
>> Hello,
>> 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:
>> # restraints
>> constraints on
>> consexp 2
>> consref res.pdb
>> conskfile restrained_res.pdb
>> conskcol O
>> 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.
>> Thanks.
>> --Julie

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