Thank you very much, Mark! The problem was for the type CG2 in .rtp. I
corrected it and the errors disappear.[?]
(I should study more for that non-zero charge, i think.)
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On 16/11/2010 9:04 PM, hengame fallah wrote:
Thank you very much, Mark!
Now i have errors from my .top file after grompp command.
The question is that why in pdb2gmx, editconf ,genbox and make_ndx
steps i don't see these errors:
...
processing topology...
Opening library file
Dear Mark,
I think that i couldn't explain my problem clearly, however i have changed
my .rtp but i don't know how should be my .hdb file.
a) The structure of *BOC* is: *-CO-CH2-CH(C6H5Cl)-CH2-NH-*
b) This is the new charges:
[ BOC ]
[ atoms ]
Nopls_238 -0.500 1
H
On 14/11/2010 7:26 PM, hengame fallah wrote:
Dear Mark,
I think that i couldn't explain my problem clearly, however i have
changed my .rtp but i don't know how should be my .hdb file.
a) The structure of *_BOC_* is: *-CO-CH2-CH(C6H5Cl)-CH2-NH-*
Great.
b) This is the new charges:
[ BOC ]
I read about .hdb file and then i editted my .hdb file:
...
BOC 9
11H N -CCA
26HA CA N CB
15HB CB CA CG1CG2
11HD1CD1CG1CE1
11HD2CD2CG1CE2
11HE1CE1CD1CZ
1
On 14/11/2010 8:13 PM, hengame fallah wrote:
I read about .hdb file and then i editted my .hdb file:
...
BOC 9
Then you'll know from your reading what this number should be :-) It's
the number of types of hydrogen atoms that might be added. For each of
them, there's one line below. You
Thanks Justin,
actually the protein that i want to simulate consists of two amino acids:
PHE and BOC
BOC is an unusual amino acid as you know.
It has a Cl instead of HZ in PHE and has one extra CH2 in comparison to PHE
I finally defined a residue BOC in opls .rtp file:
[ BOC ]
[ atoms ]
N
On 9/11/2010 8:19 PM, hengame fallah wrote:
Thanks Justin,
actually the protein that i want to simulate consists of two amino
acids: PHE and BOC
BOC is an unusual amino acid as you know.
It has a Cl instead of HZ in PHE and has one extra CH2 in comparison
to PHE
So that probably means
Dear Mark,
I edited my pdb like this:
...
ATOM 41 N BOC 3 -1.862 5.210 5.333
ATOM 42 H BOC 3 -2.325 4.344 5.618
ATOM 43 CA BOC 3 -1.001 5.232 4.169
ATOM 44 HA1 BOC 3 -0.540 6.235 4.026
ATOM 45 HA2 BOC 3
On 9/11/2010 9:09 PM, hengame fallah wrote:
Dear Mark,
I edited my pdb like this:
...
ATOM 41 N BOC 3 -1.862 5.210 5.333
ATOM 42 H BOC 3 -2.325 4.344 5.618
ATOM 43 CA BOC 3 -1.001 5.232 4.169
ATOM 44 HA1 BOC 3 -0.540
This is .rtp for [PHE] in opls:
[ PHE ]
[ atoms ]
Nopls_238 -0.500 1
Hopls_2410.300 1
CAopls_224B 0.140 1
HAopls_1400.060 1
CBopls_149 -0.005 2
HB1opls_1400.060 2
HB2opls_1400.060 2
CG
On 9/11/2010 10:10 PM, hengame fallah wrote:
This is .rtp for [PHE] in opls:
...wherein all the charge groups are neutral, unlike yours for BOC.
This will be fairly moot for a PME simulation, however.
[ PHE ]
[ atoms ]
N opls_238
hengame fallah wrote:
Hi,
I'm using the OPLS force field.
[ PHE ]
[ atoms ]
Nopls_238 -0.500 1
Hopls_2410.300 1
CAopls_224B 0.140 1
HAopls_1400.060 1
CBopls_149 -0.005 2
HB1opls_1400.060 2
HB2
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