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

[Elaine Meng]

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
>> 
>> 
>> __________ Informace od ESET NOD32 Antivirus, verze databaze 7204 (20120607) __________
>> 
>> Tuto zpravu proveril ESET NOD32 Antivirus.
>> 
>> http://www.eset.cz
>> 
>> 
>> 
> 
> 
> -- 
> Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>