On 6/27/12 2:49 PM, shounakb wrote:
Hi Shima,
i do not think pdb2gmx uses the tdb files. However, I feel that the FOR
tdb entries should go to aminoacids.c.tdb and not aminoacids.n.tdb
Both of these assertions are incorrect. The *only* Gromacs program that uses
.tdb files is pdb2gmx. The FOR cap is on the N-terminus, so it cannot be in
.c.tdb. Both .tdb files are irrelevant for this problem, as stated before.
I saw your other thread where you have described the FOR topology you added.
I think the atoms should be CA and O and their respective atom types,
CH1/CH2 and O.
This does not solve the problem. If one changes the "C" atom name to "CA" then
pdb2gmx will certainly complain that the atom "C" is missing, since improper
construction for VAL is dependent upon atoms "C" and "CA" being present in the
preceding residue.
I guess you already have partial charges for the atoms? Shouldn't that solve
the problem with VAL that Justin highlighted, without having to comment out
the impropers line?
Partial charges are irrelevant here. The error complains about an atom not
being found, not the charge on any given atom. Shima has a functional .rtp
entry for the FOR residue. It is not the problem, VAL is. Better stated, the
mechanism used by gmx.ff to generate impropers in this case blocks the use of
FOR as a separate residue, since it does not contain the same atoms as an amino
acid, specifically a C and CA.
-Justin
Regards,
Shounak
Shima Arasteh wrote
:))
I can't eliminate it, I decided to do , but when I studied about the
structure of protein ( consists of 2 monomers, which form a dimer in lipid
bilayer, and the reason of this formation is the existence of formyl
residues in N-teminals) . Then I got regretful to remove it. Don't you
agree?
Sincerely,
Shima
----- Original Message -----
From: Justin A. Lemkul <jalemkul@>
To: Discussion list for GROMACS users <gmx-users@>
Cc:
Sent: Wednesday, June 27, 2012 10:25 PM
Subject: Re: [gmx-users] Re: pdb2gmx error
On 6/27/12 1:52 PM, shounakb wrote:
Shima, I use gromacs-4.5.4. Without the FOR residue, my
gmx.ff/aminoacids.rtp
file works fine for the sequence you originally specified. (pdb2gmx
executes
without any errors)
I guess you added the FOR cap's topology yourself?
Justin, could this be an issue?
Please see the previous posts on these topics, including the post from
just a few minutes ago where I discovered the source of the problem. The
FOR residue issue has been an ongoing discussion over several weeks. I
will maintain that I do not necessarily believe that a two-atom model of a
formyl group is sufficiently accurate for a Gromos force field, since the
alpha proton is very polar and thus may need to be explicitly
represented. I have stated my skepticism before but it appears Shima is
pursuing the current course. Side note ;)
-Justin
-- ========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
-- gmx-users mailing list gmx-users@
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-request@.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request@.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
View this message in context:
http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998870.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
