[Chimera-users] TER characters between residues in exported PDB ?

[Marek Maly]

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  
prepin/frcmod files,
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  
file but
both input files: PRMTOP (ff parameters) and INPCRD (atom coordinates) are  
necessary
to start simulation in Amber.


So again I (and perhaps not only me) would be very grateful for adding  
that new
small but very useful TER feature and eventually that correction of CONECT  
records
as I described below.

  Thanks again !

      Best wishes,

          Marek






Dne Thu, 07 Jun 2012 22:25:56 +0200 Elaine Meng <meng at cgl.ucsf.edu>  
napsal/-a:

> 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.
> Best,
> Elaine
>
> 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)
>>
>> or
>>
>> branched polymer (gaff) + sugar (GLYCAM) + peptide (ff99SB)
>>
>> etc.
>>
>>
>> I am not sure if actual implementation of Amber/Antechamber module in  
>> Chimera
>> 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,
>>
>>      Marek
>>
>>
>>
>>
>>
>>
>>
>> Dne Thu, 07 Jun 2012 21:12:10 +0200 Elaine Meng <meng at cgl.ucsf.edu>  
>> napsal/-a:
>>
>>> Hi Marek,
>>> If you are going to use Amber, might as well just use Write Prmtop  
>>> instead (in menu under Tools... Amber):
>>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addions/writeprmtop.html>
>>>
>>> This saves both a prmtop file and a inpcrd file.
>>> Best,
>>> Elaine
>>> ----------
>>> 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,
>>>>
>>>>      Marek
>>>
>>>
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>>
>>
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>
>
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>
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>
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>
>
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