> Dear Acharya,
> Thank you very much for this quick reply. According to your suggestion, I
> measure the main chain dihedral angles, only to find that same values are
> obtained for both isotactic and syndiotactic ones.
That is obvious i think for a correct tacticity polymeric chain.
> Therefore,
Hello
I think constraining rotation about all the main chain bonds should be
sufficient to preserve the tacticity. So taking your example, the dihedral
angles could be R1 C1 C2 C1 and C1 C2 C1 R2. Of course you will have
restrain all similar dihedral angles along the whole length of your
polymer.
d also the tau_t : 01. 01. Can u
> explain it why?
this has been explained quite clearly in the gromacs manual. In essence,
defining different coupling groups allows control over the temperature of
the Groups especially protein and water which otherwise have been seen to
differ in the temperature att
49 of the box length in the particular
direction. That is what the error is all about.
So if you need to pull in all three directions by a particular distance,
then make sure that the box length in all directions are greater than
twice the pull distance.
Cheers
Abhishek Acharya
Structura
Hello George,
You need to use Antechamber, a software provided by the amber developers
in a free Amber Tools package. That will produce the right parameters for
the Amber force feild.
Cheers
Abhishek
Hello Joao
>
> Thanks for the reply; I am planning to use Amber 99SB-ILDN force field.
>
> I jus
> Again and again posting from Abhishek Acharya or Shima, or Rama David or
> somehow else ... pls read my posting before, it could be useful for you,
> Indian fellows ... maybe it's possible to get some kind of agreement
> though brahmin.net or so ..
>
> Best regards of so
nc 0.15 -neutral
(incase you want a NaCl conc of 0.15 M. Only in this case, genion will
automatically add NA and CL ions to neutralize the charge and sufficiently
reach the given conc., in this case 0.15 M)
Cheers.
Abhishek Acharya
Structural and Computational Biology Lab
Indian Institu
re a
> solvent molecule couldn't quite fit... :-)
>
> Mark
>
> On Fri, Mar 15, 2013 at 7:48 AM, Abhishek Acharya
> wrote:
>
>> Hello Gromacs Users.
>> I ran an NVT simulation and i noticed that after the initial step at
>> 300K
>> the temperatur
) Constr. rmsd
1.95652e+03 -2.24892e+021.49190e+042.42873e-05
With Regards
Abhishek Acharya
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appropriately (or not
> calling
> the right MPI wrapper compiler) might cause symptoms like yours, we need
> more complete information to have a chance of helping solve your problem.
> Christoph also asked for your cmake command line.
>
> Mark
>
> On Mon, Mar 4, 2013 at 9:04 PM,
that also gave me the same error.
In any case, gromacs4.6 got installed properly by disabling shared
libraries and is up and running. Though i would be interested in knowing
if its possible to remove this error in any other way.
with regards
Abhishek
>
> On Sat, Mar 2, 2013 at 7:20 AM, A
>> Date: Fri, 1 Mar 2013 23:59:36 +0530
>> From: "Abhishek Acharya"
>> Subject: [gmx-users] Installation Problems with Gromacs4.6
>> To: "gromacs maillist"
>> Message-ID:
>> <2ca7063e41d6ddfa7ea411dc3cfe3ad3.squir...@webmail
g 4.5.6 and it got installed without any
such problems. I need 4.6 because my tpr files are produced in Gromacs4.6
and I am using the Verlet cutoff scheme.
Thanks in advance
With Regards
Abhishek Acharya
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>
>
> On 2/15/13 4:00 PM, Abhishek Acharya wrote:
>>
>>
>>>
>>> On 2/15/13 1:29 PM, Abhishek Acharya wrote:
>>>> Dear GROMACS Users.
>>>> Just out of curiosity, i would like to pose a general question here (
>>>> i
My thoughts are like any other residue in protein, for Mg ion ang GDP/GTP
also, the standard charges should be able to govern the energetics and
hence the movements in the protein properly. Not sure, how much of a
difference would the change in charges due to polarization effects of Mg
ion make
>
> On 2/15/13 1:29 PM, Abhishek Acharya wrote:
>> Dear GROMACS Users.
>> Just out of curiosity, i would like to pose a general question here ( i
>> didn't have an idea of any other suitable forum ). My protein active
>> site
>> has a GDP which is c
vance
With Regards
Abhishek Acharya
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>
> On 2/14/13 4:15 PM, Abhishek Acharya wrote:
>>
>>
>>> Hello Justin
>>> Thank you very much for your effort and help. I will try adding new
>>> parameter corresponding to the errors. Meanwhile just out of curiosity
>>> and
>>>
234]:
>>>No default Ryckaert-Bell. types
>>>
>>
>> So this one is HC-CT-CT-NA
>>
>>>
>>> ERROR 2 [file p2gout_GDP.itp, line 236]:
>>>No default Ryckaert-Bell. types
>>>
>>
>> OH-CT-CT-NA
>>
>>&g
dihedrals section of ffbonded.itp. How do we calculate these parameters
for new dihedrals ?
Thank you again
With regards
Abhishek
>
> On 2/12/13 6:19 AM, Abhishek Acharya wrote:
>> Hello Justin.
>> Help would really be appreciated. And yes you are correct and i
>> thought the
rrors
---
Thank you
With Regards
Abhishek Acharya
> Dear Gromacs Users.
> I generated a topology file of GDP for OPLSAA force field using MKTOP. But
> on running grompp I got a list of No default Angle types and No default
> Ryc
remained on re-run.
Is there anything wrong with this ? Do i need to edit some other related
files.
I am very new to gromacs. Kindly help as I'm stuck.
Thanks in advance.
Abhishek Acharya
M.Tech
Structural Biology Lab
Biological Sciences and Bioengineering Department
Indian Institute of Techno
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