On 4/30/15 11:28 AM, Mary Less wrote:
Dear Justin,
Thank you for your reply.
I am trying to write an opls unied atom forcefield for Tetrahydrofuran (THF). I
thought the common way to write a forcefield
is to consider the atomtypes in the atomtypes.atp and choose those types which
are suitable f
April 2015 um 14:48 Uhr
Von: "Justin Lemkul"
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] OPLS force field issue
On 4/30/15 4:46 AM, Mary wrote:
> Dear gmx users,
>
> I also try to use the OPLS force field for my simulations. After defining
> suitable atomtypes:
On 4/30/15 4:46 AM, Mary wrote:
Dear gmx users,
I also try to use the OPLS force field for my simulations. After defining
suitable atomtypes:
opls_110 (type C2)
opls_071 (type C2)
I would like to add the suitable bondtypes, angletypes and so on. But where
do I get those parameters for the an
On 2/4/14, 9:43 PM, Sidath Wijesinghe wrote:
yes it worked. i only added CA CA CZ CZ 0.000 0.000 0.000 0.000 in diheadral
block. since all 12 errors point the same kind of diheadral type.
How did you decide these parameters were appropriate? You're essentially saying
that the rotational b
yes it worked. i only added CA CA CZ CZ 0.000 0.000 0.000 0.000 in diheadral
block. since all 12 errors point the same kind of diheadral type.
Then i tried to mdrun...i got this error message
Fatal error:
1 particles communicated to PME node 6 are more than 2/3 times the cut-off
out of the d
On 2/3/14, 10:14 PM, Sidath Wijesinghe wrote:
Justin,,
i rechecked the opls/ff that i used and found some errors, after correction them
i got the .top file.
note that i was able to define the charge groups as well. when i use this .top
file with grompp,
now am getting 12 errors...as follwos..
Justin,,
i rechecked the opls/ff that i used and found some errors, after correction
them i got the .top file.
note that i was able to define the charge groups as well. when i use this
.top file with grompp,
now am getting 12 errors...as follwos..
ERROR 1 [file topol.top, line 1399]:
No defaul
On 1/22/14, 4:03 PM, Sidath Wijesinghe wrote:
1. could you please tell me what does this mean ? " charge group is
inappropriately large" the overall charge is appear to zero in my topology. i
am little confused here.
Manual section 3.4.2. If you are using the Verlet cutoff scheme, it's not
1. could you please tell me what does this mean ? " charge group is
inappropriately large" the overall charge is appear to zero in my
topology. i am little confused here.
2. if below atoms types in represent C 1&11...so on and those atom types
appear in the error
Copls_240012.0
On 1/22/14, 1:06 PM, Sidath Wijesinghe wrote:
Justin,
i was able to generate the .top file for 3 monomers by making the corresponding
.rtp entry.
below is a segment of my .rtp entry and thr .pdb file i used.
.rtp entry for first few atoms out of 208
[ UNK ]
[ atoms ]
C1 opls_24
Justin,
i was able to generate the .top file for 3 monomers by making the
corresponding .rtp entry.
below is a segment of my .rtp entry and thr .pdb file i used.
.rtp entry for first few atoms out of 208
[ UNK ]
[ atoms ]
C1 opls_2400 1
C2 opls_145-0.12 1
On 1/10/14, 2:20 PM, Sidath Wijesinghe wrote:
Justin,
i was able to obtain the . top file for 3 uncharged monomers. then i used the
grompp
i got a fatal error as follows
Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 175
Fatal error:
The largest charge group contains 2
Justin,
i was able to obtain the . top file for 3 uncharged monomers. then i used
the grompp
i got a fatal error as follows
Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 175
Fatal error:
The largest charge group contains 207 atoms. The maximum is 32.
For more information
yes that was the .top file i have used. ok..
Thank you!
On Fri, Dec 20, 2013 at 2:23 PM, Justin Lemkul wrote:
>
>
> On 12/20/13 2:20 PM, Sidath Wijesinghe wrote:
>
>> Justin,
>>
>> i went for the option 4 that u pointed out. let me explain what i did,
>>
>> i converted the .pdb file in to .gro
On 12/20/13 2:20 PM, Sidath Wijesinghe wrote:
Justin,
i went for the option 4 that u pointed out. let me explain what i did,
i converted the .pdb file in to .gro by using.
editconf -f test.pdb -o test.gro -box 18 18 18 -angles 90 90 90
then i use the text editor as follows.
Include forcef
Justin,
i went for the option 4 that u pointed out. let me explain what i did,
i converted the .pdb file in to .gro by using.
editconf -f test.pdb -o test.gro -box 18 18 18 -angles 90 90 90
then i use the text editor as follows.
Include forcefield parameters
#include "oplsaa.ff/forcefield.itp
On 12/18/13 10:13 PM, Sidath Wijesinghe wrote:
could you please give me a hint about a suitable method for this task?
You can make just about anything work.
1. pdb2gmx with .rtp entries for each of your molecules, with appropriately
named (unique) atoms
2. g_x2top can also process each dif
could you please give me a hint about a suitable method for this task?
thank you!
On Wed, Dec 18, 2013 at 9:50 PM, Justin Lemkul wrote:
>
>
> On 12/18/13 9:46 PM, Sidath Wijesinghe wrote:
>
>> Is g_x2top the only way for my situation? or am i in the wrong track?
>>
>>
> There are numerous w
On 12/18/13 9:46 PM, Sidath Wijesinghe wrote:
Is g_x2top the only way for my situation? or am i in the wrong track?
There are numerous ways to generate topologies. I have warned you that g_x2top
is probably ill-suited for this task. It works well for simple things. It does
not work w
Is g_x2top the only way for my situation? or am i in the wrong track?
if i find the parameters for the missing parameters how can i get rid of
sodium as u mentioned
for the real system with Na+ ions?
Thank you!
On Wed, Dec 18, 2013 at 9:37 PM, Justin Lemkul wrote:
>
>
> On 12/18/13 9:32 PM,
On 12/18/13 9:32 PM, Sidath Wijesinghe wrote:
Justin,
As i understood from reading and tutorial what i should do is, lets say i
generated a topology file named as
topol.top, so i need to add #include "oplsaa.ff/ions.itp" so it accounts
for Na+.
my question is..
1.how can i get rid of sodium?
Justin,
As i understood from reading and tutorial what i should do is, lets say i
generated a topology file named as
topol.top, so i need to add #include "oplsaa.ff/ions.itp" so it accounts for
Na+.
my question is..
1.how can i get rid of sodium? just removing the corresponding lines from
the .p
Justin,
As i understood from reading and tutorial what i should do is, lets say i
generated a topology file named as
topol.top, so i need to add #include "oplsaa.ff/ions.itp" so it accounts
for Na+.
my question is..
1.how can i get rid of sodium? just removing the corresponding lines from
the .p
Thank you very much!
On Tue, Dec 17, 2013 at 10:25 AM, Justin Lemkul wrote:
> On Tue, Dec 17, 2013 at 10:09 AM, Sidath Wijesinghe
> wrote:
>
> > Justin,
> >
> > so that means delete these lines "
> > ATOM 7882 SOD UNK 1 42.69 -261.86 64.056 1.00 0.00
> > UNK
> > ATOM 7883 SO
On Tue, Dec 17, 2013 at 10:09 AM, Sidath Wijesinghe
wrote:
> Justin,
>
> so that means delete these lines "
> ATOM 7882 SOD UNK 1 42.69 -261.86 64.056 1.00 0.00
> UNK
> ATOM 7883 SOD UNK 1 39.09 -260.89 62.8968 1.00 0.00 UNK
> ATOM 7884 SOD UNK 1 40
Justin,
so that means delete these lines "
ATOM 7882 SOD UNK 1 42.69 -261.86 64.056 1.00 0.00 UNK
ATOM 7883 SOD UNK 1 39.09 -260.89 62.8968 1.00 0.00 UNK
ATOM 7884 SOD UNK 1 40.1388 -263.52 64.6776 1.00 0.00 UNK
ATOM 7885 SOD UNK 1
On Mon, Dec 16, 2013 at 11:26 PM, sidath1 wrote:
> Justin,
>
> i have added these few lines to the atomname2type.n2t
>
> Copls_240012.0113C 0.142 C 0.142 C 0.142
> Copls_239012.0112C 0.142 C 0.142
>
> O opls_267 -0.495284 15.9994 1 C 0.1214
>
>
Justin,
i have added these few lines to the atomname2type.n2t
Copls_240012.0113C 0.142 C 0.142 C 0.142
Copls_239012.0112C 0.142 C 0.142
O opls_267 -0.495284 15.9994 1 C 0.1214
C opls_4700.594326 12.0110 3 C 0.1487 O 0.1306 O 0.1
On Mon, Dec 16, 2013 at 8:09 PM, Sidath Wijesinghe wrote:
> Justin,
>
> Thank you for the reply. so that means i need to place the parameters in
> atomname2type.n2t file?
>
>
Yes, per the format shown on that site. I will warn you that it can be
difficult to define non-overlapping parameters for l
Justin,
Thank you for the reply. so that means i need to place the parameters in
atomname2type.n2t file?
i am little confused here
Thank you!
Sidath
On Mon, Dec 16, 2013 at 4:11 PM, Justin Lemkul wrote:
> On Mon, Dec 16, 2013 at 4:06 PM, Sidath Wijesinghe >wrote:
>
> > Dear Friends,
>
On Mon, Dec 16, 2013 at 4:06 PM, Sidath Wijesinghe wrote:
> Dear Friends,
>
> i have done a MD simulation using OPLS/AA in lammps which contains 7930
> atoms.
> i want to run this in Gromacs
>
> so i followed this step
>
> g_x2top -f test.pdb -o np1.top -name np1 -ff oplsaa -pbc ( test.pdb is the
On Mon, Dec 9, 2013 at 3:05 PM, Ehsan Sadeghi wrote:
> Thanks Justin.
>
> I added the bond description in the ffbonded.itp but it does not show in
> the topol.top file.
>
> In ffbonded.itp we have:
>
> [ bondtypes ]
> ; ij func b0 kb
> OWHW 10.09572 502080.0
lot,
Ehsan
- Original Message -
From: "Justin Lemkul"
To: gmx-us...@gromacs.org
Sent: Friday, December 6, 2013 11:28:01 AM
Subject: Re: [gmx-users] OPLS force field issue
On 12/6/13 1:46 PM, Ehsan Sadeghi wrote:
> Hi gmx users,
>
> I try to use OPLS force field f
Hi,
if you create the topol.top with 'pdb2gmx', the values for all the
parameters are not listed in the topology. Only all the atom numbers,
from these GROMACS can search the atom- and/or bondtypes and then it
constructs the bonded parameters. If any parameters are missing 'grompp'
will compla
On 12/6/13 1:46 PM, Ehsan Sadeghi wrote:
Hi gmx users,
I try to use OPLS force field for my simulation. I added the following residue
to the aminoacids.rtp, but when I generate the topol.top file it does not show
the the bond stretching, angle bond, dihedrals. Where should I add these
prope
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