Hi, Jodi. Thank you so much for your help.
I have 12 ligands with the common scaffold. Some pairs with only one or
two atoms that are different can work fine. Some pairs with more than 5
different atoms different (scmask atoms more than 5) cannot work without
manipulating the order. Sorry for the unclearness. I need to make them
all work.
Best regards,
Joyce Huang
On Tue, Oct 30, 2012 at 4:48 PM, Jodi Ann Hadden <jodih.uga.edu> wrote:
> Hi Joyce,
>
> This seems like an unnecessary complication.
>
> Since you are doing TI in AMBER11, I assume you are using soft core
> potentials instead of the dummy atom method, and you have separate topology
> files that represent the lambda=0 and lambda=1 end states. In this case,
> you only have to make sure the common atoms from each state are in the same
> order in the two separate files, that is, the atoms that are not going in
> your scmask. If the common atoms are in the same relative order, but just
> have scmask atoms in between them, that is fine. Everything else just has
> to be the same ignoring scmask atoms. Since your scmask is only one or to
> atoms, this should be pretty easy to ensure without excessive file
> manipulation. You don't have to move the ligand differences to the end of
> the file as long as you are specifying them in your scmask.
>
> Hope this helps,
> Jodi
>
> Jodi Hadden
> GLYCAM Lab
> Complex Carbohydrate Research Center
> University of Georgia
>
>
> On Oct 29, 2012, at 10:35 AM, Yulin Huang <yulinhuang2007.gmail.com
> <mailto:yulinhuang2007.gmail.com>> wrote:
>
> Dear Amber users:
> I am performing binding free energy calculation for a kinase with
> 12 ligands using thermodynamic integration (AMBER11). It seems that the
> atom names and orders for the corresponding atoms in these 12 ligands in
> the initial setup have to be the same. Thus the
> parm files and crd files generated after I use the antechamber, parmchk
> could be the same
> for the corresponding atoms. After that, the small mask (one or two atoms)
> can be specified for calculations.
>
> I have manually made all the corresponding atom names the same. Now I am
> trying to make the order the same. It is not an easy task. The way I do is
> to put all the different atoms among 12 ligands at the end of ligand mol2
> files. But I have to change all the connectivity part. I've tried to load
> the mol2 file into software MOE and output the pdb file and then convert to
> mol2 file. But the different atom such as O will be placed in the middle
> of the mol2 file automatically. But I have to put the different atoms in
> the end to make the corresponding atoms in the same order.
>
> Does anyone has any ideas for this problems? Many thanks in advance.
>
> --
> Yulin "Joyce" Huang
> Ph.D Candidate
> Computational Chemistry (CADD)
> Advisor: Dr. Robert C. Rizzo
> State University of New York at Stony Brook
> Stony Brook NY,11790
> Office: (631)632-8519
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--
Yulin "Joyce" Huang
Ph.D Candidate
Computational Chemistry (CADD)
Advisor: Dr. Robert C. Rizzo
State University of New York at Stony Brook
Stony Brook NY,11790
Office: (631)632-8519
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Received on Wed Oct 31 2012 - 08:30:03 PDT
