For what it may be worth, the http://www.somewhereville.com/?p=114
page has had its ion.itp content corrected and, hopefully, it is now a
little less useless than it was yesterday. Having fought a bit with
the install process myself, I hope people find the ffamber/gromacs
page of use and if they find errors or concerns to please bring them
up (thanks Alan!).
Damian Allis
Locale : www.somewhereville.com
Delivery : [EMAIL PROTECTED]
Skype : somewhereville
AOL IM : swville
On Jul 8, 2008, at 4:40 AM, Alan wrote:
Answering my self:
My ions.itp file was wrong. The correction is:
[ atoms ]
; id type resnr residue atom cgnr charge
mass
1 amber99_30 1 Cl Cl 1 -1
35.45000
#endif
and so on.
Since I got my ions.itp from amber_ions.txt from
http://www.somewhereville.com/?p=114 it's also wrong there.
Basically, the error is that column cgnr is exchanged with column
charge.
"Caveat Emptor"
Cheers,
Alan
On Thu, Jul 3, 2008 at 7:44 AM, Alan <[EMAIL PROTECTED]> wrote:
Hi List,
To people using ffamber.
I have ffamber with ions.itp modified to recognise ffamber ions.
All seems
fine and working.
So, I have a protein, net charge +4 e. In the pdb file there no
ions and no
water. I modify the pdb as said in ffamber instructions. All fine.
Then, I add water and hence I use genion to neutralise my system. I
add 4
Cl. All fine.
However when using grompp for preparing the inputs for a
minimisation, I got
a warning saying that my system is now +8 e. It happens no matter
what ion I
use with ffamber (being it pos or neg, or value 2). It's like if
genion were
counting only the ions and not reading the ion's charge value.
I know it's reading my modified ions.itp file because otherwise
genion will
fail to process.
Has someone else seen that? Any comments?
Despite this, I can minimise and carry on MD on my system. Is there
any
other to definitely know if GMX is computing the right charge values?
Many thanks in advance.
Cheers,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28<<
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28<<
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#8^(=)+<, ph.d.
p.s. Damian apologizes for the delay.
p.p.s. Have you backed up lately?
Locale : www.somewhereville.com
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