irene farabella wrote:
Hello Gmx Usrs,
I am new to Gromacs. I am trying to simulate a protein-membrane
complex using berger-oplsaa combination . I have created a topology
Have you properly modified the Berger parameters for use with OPLS-AA?
Otherwise, the results you will get will be nonsense :)
file for the protein using pdb2gmx in order to then build up the
topology for my system using the include file mechanism.
After that I tried to use my system.top in grompp ( grompp -f xx.mdp
-c system.pdb -p system.top -o out.tpr ) but I get a warning about
atoms in top and pdb does not match. I went trough the mailing list
Is system.pdb the cleaned up output from pdb2gmx?
It is also better to post the actual error message. The topology and coordinate
file may not match in terms of atom names or in terms of the number of
coordinates, which are both very different problems. I guess you are referring
to a naming mismatch?
but I have still doubt. I checked where were the differences. It seems
that the order of the aromatic ring in the pdb and in the top didn't
match.
To be clear (tyr as example but the same problem occur with his):
.pdb .top
N N
HN H
If this is what's in your .pdb file, then you aren't using the pdb2gmx output,
are you?
CA CA
HA HA
CB CB
HB1 HB1
HB2 HB2
CG CG
CD1 CD1
HD1 HD1
CE1 CD2
HE1 HD2
CZ CE1
OH HE1
HH CE2
CD2 HE2
HD2 CZ
CE2 OH
HE2 HH
C C
O O
Is this because the .top seems follow the order presents in the rtp
file that I have (am I right?).
Yes, pdb2gmx will output according to the .rtp entry.
Assuming that this is the case I am wondering if changing the atoms
order in the rtp from:
[ TYR ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_149 -0.005 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_145 -0.115 3
CD1 opls_145 -0.115 4
HD1 opls_146 0.115 4
CD2 opls_145 -0.115 5
HD2 opls_146 0.115 5
CE1 opls_145 -0.115 6
HE1 opls_146 0.115 6
CE2 opls_145 -0.115 7
HE2 opls_146 0.115 7
CZ opls_166 0.150 8
OH opls_167 -0.585 8
HH opls_168 0.435 8
C opls_235 0.500 9
O opls_236 -0.500 9
to:
[ TYR ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_149 -0.005 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_145 -0.115 3
CD1 opls_145 -0.115 4
HD1 opls_146 0.115 4
CE1 opls_145 -0.115 6
HE1 opls_146 0.115 6
CZ opls_166 0.150 8
OH opls_167 -0.585 8
HH opls_168 0.435 8
CE2 opls_145 -0.115 7
HE2 opls_146 0.115 7
CD2 opls_145 -0.115 5
HD2 opls_146 0.115 5
C opls_235 0.500 9
O opls_236 -0.500 9
can that have a further effect since it seems that the file handling
is based on line position and not atoms name.
If you re-arrange the .rtp file, you'll have to start all over again, since only
pdb2gmx uses the .rtp files. I doubt this is meaningful. If you've got a
.pdb file with HN as the amide proton, then it won't match the topology, which
specifies this atom as H. There will still be a name mismatch, but not an order
mismatch, which simply indicates to me that you are using the wrong coordinate file.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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