hengame fallah wrote:
Hi,
I'm using the OPLS force field.
[ PHE ]
[ 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 2
CD1 opls_145 -0.115 3
HD1 opls_146 0.115 3
CD2 opls_145 -0.115 4
HD2 opls_146 0.115 4
CE1 opls_145 -0.115 5
HE1 opls_146 0.115 5
CE2 opls_145 -0.115 6
HE2 opls_146 0.115 6
CZ opls_145 -0.115 7
HZ opls_146 0.115 7
C opls_235 0.500 8
O opls_236 -0.500 8
I want to attach "CL" atom instead of HZ
i made my pdb but when i use pdb2gmx, it adds HZ automatically in gro
and top files.
What should i do to get rid of this HZ and attach CL instead.
If the .rtp entry says to build PHE with those constituent atoms, it will do so.
You can make a custom .rtp entry that has CL instead of HZ.
(I edited top and gro files and remove HZ from them, it seemed to work
properly at first, but when i tried to do energy minimization, it had
errors in top file
and i realized that it couldn't recognized the bond between CL and CZ):
ERROR 1 [file topol.top, line 150]:
No default Bond types
ERROR 2 [file topol.top, line 422]:
No default Angle types
ERROR 3 [file topol.top, line 423]:
No default Angle types
All of these errors indicate that OPLS cannot accommodate such a species.
Making ad hoc changes to the topology often does this. Look at what these lines
contain and you will be able to identify the relevant parameters that are missing.
<snip>
66 opls_401 5 CL CL 26 -1 35.453
; qtot -1.06
I would seriously question the validity of doing this. Is it really correct to
put (essentially) a Cl- ion on a Phe ring and call it correct? Proper
parameterization is a very challenging task, and I doubt what you've proposed
here is valid.
http://www.gromacs.org/Documentation/How-tos/Parameterization
-Justin
...
[ bonds ]
...
59 66 1
60 61 1
60 62 1
63 64 1
63 65 1
...
[ angles ]
...
58 57 59 1
55 59 57 1
55 59 66 1
57 59 66 1
45 60 61 1
45 60 62 1
61 60 62 1
64 63 65 1
...
--
========================================
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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