[Chimera-users] TER characters between residues in exported PDB ?
marek.maly at ujep.cz
Thu Jun 7 13:48:26 PDT 2012
Yes I see,
but these are the reasons:
(actually absent of GAFF, impossiblity to use more specialized ff like
GLYCAM, impossibility to use contributed
libraries (e.g. for metaloproteines), impossibility to use already created
impossibility to use ff mixtures)
why in such a complicated systems one have to proceed by the classical way
i.e. direct using of
Antechamber in Amber.
I also found (in actual alpha version) just possibility to save PRMTOP
both input files: PRMTOP (ff parameters) and INPCRD (atom coordinates) are
to start simulation in Amber.
So again I (and perhaps not only me) would be very grateful for adding
small but very useful TER feature and eventually that correction of CONECT
as I described below.
Thanks again !
Dne Thu, 07 Jun 2012 22:25:56 +0200 Elaine Meng <meng at cgl.ucsf.edu>
> Hi Marek,
> Chimera will use gaff for nonstandard residues and your chosen force
> field for standard residues, but it does not know about carbohydrates
> and GLYCAM. I believe it would lump them with the other nonstandard
> residues (use gaff/Antechamber).
> I don't think there is any way to tell Chimera to also use your own
> frcmod files.
> Also, in the current daily build, ff12SB is recommended and ff99*
> deprecated (has been removed from the Add Charge GUI, although still
> available in the addcharge command). There is some discussion in the
> Ambertools12 manual about why the ff99* versions are deprecated.
> On Jun 7, 2012, at 1:12 PM, Marek Maly wrote:
>> Dear Elaine,
>> thanks for your prompt information !
>> Unfortunately systems which I am simulating are not so simple
>> usually are composed of several parts for which different
>> ff should be used e.g.
>> example system = branched polymer (gaff) + DNA (ff99bsc0)
>> branched polymer (gaff) + sugar (GLYCAM) + peptide (ff99SB)
>> I am not sure if actual implementation of Amber/Antechamber module in
>> can manage such nontrivial systems.
>> Another thing I have already for my GAFF-param molecules "prepin" and
>> "frcmod" files (wider library for different molecular segments). Is
>> Chimera somehow
>> able to accept them when creating prmtop and incprd files of the given
>> system ?
>> I think that to add into "Save PDB" dialog just one more option
>> ("Separate residues by TERs") should be easy work but very valuable
>> for guys like me, otherwise we have to use own post-processing which
>> takes some additional time.
>> I noticed also another thing which creates a small troubles. If I load
>> in Chimera system AB then delete in Chimera part B and save the rest
>> (part A)
>> as the PDB file there still remain CONECT records which belongs to
>> deleted atoms B. If there is no important reason for this, might
>> be this also corrected as there are again problems in Amber ("Illegal
>> CONECT record in pdb file") in that case so one have to
>> correct it manually each time.
>> Thank you very much in advance !
>> Best wishes,
>> Dne Thu, 07 Jun 2012 21:12:10 +0200 Elaine Meng <meng at cgl.ucsf.edu>
>>> Hi Marek,
>>> If you are going to use Amber, might as well just use Write Prmtop
>>> instead (in menu under Tools... Amber):
>>> This saves both a prmtop file and a inpcrd file.
>>> Elaine C. Meng, Ph.D.
>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> On Jun 7, 2012, at 11:19 AM, Marek Maly wrote:
>>>> Hello all,
>>>> I would like to know if there is any way how to export from Chimera
>>>> molecular structure in PDB format
>>>> but with TER string between all residues in the file.
>>>> This would be very helpful if one prepares in Chimera PDB inputs
>>>> (containing also non protein or non DNA/RNA molecules)
>>>> for Amber because Amber (Leap) automatically tries to create bonds
>>>> between all consecutive residues unless they are separated
>>>> by TER string.
>>>> Thank you very much for any useful information.
>>>> Best wishes,
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> (20120607) __________
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