On 12/12/15 1:59 PM, gromacs query wrote:
Due to reasons, would it be possible for you to suggest off-list? I will
really appreciate.
Sure, send me coordinates and your current topology.
-Justin
Thanks.
On Sat, Dec 12, 2015 at 6:35 PM, Justin Lemkul wrote:
On 12/12/15 1:25 PM, groma
Due to reasons, would it be possible for you to suggest off-list? I will
really appreciate.
Thanks.
On Sat, Dec 12, 2015 at 6:35 PM, Justin Lemkul wrote:
>
>
> On 12/12/15 1:25 PM, gromacs query wrote:
>
>> Hi Justin
>>
>> Somehow I can not use available units in CHARMM library. The best thing
On 12/12/15 1:25 PM, gromacs query wrote:
Hi Justin
Somehow I can not use available units in CHARMM library. The best thing I
could achieve as of now is using CGenFF. I created a side chain terminated
with some atoms (cap) which are same as in the next attaching unit
(directly available in CHA
Hi Justin
Somehow I can not use available units in CHARMM library. The best thing I
could achieve as of now is using CGenFF. I created a side chain terminated
with some atoms (cap) which are same as in the next attaching unit
(directly available in CHARMM). After removing caps from the side chain
On 12/11/15 2:20 PM, gromacs query wrote:
Hi Justin
Thanks for the explanation. Just few things.
1) When you say " Initial charge fitting would be done on a side chain ..."
you mean using some QM method? Which seems expensive and needs expertise
which I dont have.
Yes, these are generally
Hi Justin
Thanks for the explanation. Just few things.
1) When you say " Initial charge fitting would be done on a side chain ..."
you mean using some QM method? Which seems expensive and needs expertise
which I dont have.
2) Also, as you said assigning charges and types with analogy does this
m
On 12/11/15 1:28 PM, gromacs query wrote:
Hi Justin
I am bit lost I think. For e.g. in the amino acid residues library we have
-CO-CH(R)-NH- which we can combine these amino acids in any way and in the
rtp file it defines only these atoms and connecting atoms are mentioned
specifically.
Now l
Hi Justin
I am bit lost I think. For e.g. in the amino acid residues library we have
-CO-CH(R)-NH- which we can combine these amino acids in any way and in the
rtp file it defines only these atoms and connecting atoms are mentioned
specifically.
Now lets say I have some new amino acid -CO-CH(X)-N
On 12/11/15 12:17 PM, gromacs query wrote:
Hi Justin
Thanks for the reply. Yes your are right and indeed, sorry I forgot to
mention, I tried with some CH3 and other groups which may be considered as
an appropriate 'cap' which is normally followed by many. But in this case I
will have to remove
Hi Justin
Thanks for the reply. Yes your are right and indeed, sorry I forgot to
mention, I tried with some CH3 and other groups which may be considered as
an appropriate 'cap' which is normally followed by many. But in this case I
will have to remove the cap e.g. B-O-CH3 to B-O- before joining to
On 12/11/15 10:17 AM, gromacs query wrote:
Hi All,
I am using cgenff to derive parameters for some polymer (A-...-C). The
repeating block B has some Oxygen O atom which joins the next residue
(-BO-). When I derive charges for B residue with cgenff then I get net -1
charge on B residue beca
Hi All,
I am using cgenff to derive parameters for some polymer (A-...-C). The
repeating block B has some Oxygen O atom which joins the next residue
(-BO-). When I derive charges for B residue with cgenff then I get net -1
charge on B residue because of this unsatsified O atom. I want to keep
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