Thanks everyone for the help. I tried many methods, but I realize I have
to have prep files in the same order for TI. Even I built the mol2, pdb
files with the same order for corresponding atoms, I still have different
prep files which cause the problem. Does anyone has the experience of
mapping one prep file to the other one with the same atoms in the order?
Thanks.
On Wed, Oct 31, 2012 at 10:10 PM, Yulin Huang <yulinhuang2007.gmail.com>wrote:
> Thanks for everyone's suggestion. But our lab uses a specific script to
> obtain ligand charges at the HF/6-31G* level of theory using the ChelpG60
> method as implemented in Gaussian98. I need mol2 files to run this script
> and after this, all the atom names and orders have changed. The only way
> is to do everything manually and place different atoms at the end of the
> file. Because I have to use mol2 files with charges to obtain crd and
> parm. Or I have to use a series of different scripts to do this.
>
> On Wed, Oct 31, 2012 at 12:17 PM, Yulin Huang <yulinhuang2007.gmail.com>wrote:
>
>> Hi, Dan. Thank you so much for your help. This is a great way to try
>> this. Thanks.
>>
>> Joyce
>>
>>
>> On Wed, Oct 31, 2012 at 11:43 AM, Daniel Roe <daniel.r.roe.gmail.com>wrote:
>>
>>> Hi,
>>>
>>> You could try the 'atommap' command in Cpptraj, which employs a simple
>>> algorithm to reorder a target structure according to an origin
>>> structure based on bonding patterns. As long as your ligand is not too
>>> large (<100 atoms or so) and the # of atoms in target and origin are
>>> fairly close the algorithm works pretty well.
>>>
>>> Say your target is target.pdb and the origin you want it to map to is
>>> origin.pdb; the command sequence is:
>>>
>>> parm target.pdb [target]
>>> reference target.pdb parm [target]
>>> parm origin.pdb [origin]
>>> reference origin.pdb parm [origin]
>>>
>>> atommap target.pdb origin.pdb mapout atommap.dat # This creates the atom
>>> map
>>>
>>> trajin target.pdb parm [target]
>>> trajout reordered.pdb parm [target] # This will print out target.pdb
>>> reordered according to origin.pdb
>>>
>>> Hope this helps, let me know if you try it and run into problems.
>>>
>>> -Dan
>>>
>>>
>>> On Wed, Oct 31, 2012 at 2:35 AM, <steinbrt.rci.rutgers.edu> wrote:
>>> > Hi Joyce,
>>> >
>>> > in case the ligand files come from some third party software that does
>>> > completely mix up the atom order (e.g. because an additional group
>>> changes
>>> > the numbering order in a ring), there is probably really no way around
>>> > rebuilding them by hand.
>>> >
>>> > When ligands are fairly similar it may help to draw their common core
>>> in
>>> > xleap, save that fragment and then build each ligand from the fragment
>>> and
>>> > saving it as mol2. I think the common atom order will be the same in
>>> that
>>> > case.
>>> >
>>> > Take care, when you run such a ligand through antechamber, e.g. for
>>> > charges, it may reorder the atoms again. Some hand
>>> manipulation/checking
>>> > is certainly involved in this, I think there is no reliable automated
>>> way
>>> > yet. This may change in Amber13, though...
>>> >
>>> > Kind Regards,
>>> >
>>> > Thomas
>>> >
>>> > On Tue, October 30, 2012 4:48 pm, Jodi Ann Hadden 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
>>> >> _______________________________________________
>>> >> AMBER mailing list
>>> >> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
>>> >> http://lists.ambermd.org/mailman/listinfo/amber
>>> >>
>>> >>
>>> >>
>>> >> _______________________________________________
>>> >> AMBER mailing list
>>> >> AMBER.ambermd.org
>>> >> http://lists.ambermd.org/mailman/listinfo/amber
>>> >>
>>> >
>>> >
>>> > Dr. Thomas Steinbrecher
>>> > formerly at the
>>> > BioMaps Institute
>>> > Rutgers University
>>> > 610 Taylor Rd.
>>> > Piscataway, NJ 08854
>>> >
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
>>> --
>>> -------------------------
>>> Daniel R. Roe, PhD
>>> Department of Medicinal Chemistry
>>> University of Utah
>>> 30 South 2000 East, Room 201
>>> Salt Lake City, UT 84112-5820
>>> http://home.chpc.utah.edu/~cheatham/
>>> (801) 587-9652
>>> (801) 585-9119 (Fax)
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> 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
>>
>
>
>
> --
> 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
>
--
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 Tue Nov 06 2012 - 07:30:03 PST
