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

Marek Maly marek.maly at ujep.cz
Thu Jun 7 13:12:54 PDT 2012

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):
> <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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