hello Ross:
I confirmed that I also found this problem.
I think the biggest problem is not the format of the PDB but how did
Amber treat those residues during the simulations. If it treat the
split three moeity of a lipids as a whole , it should be OK. Otherwise,
it would be a big problem for the simulation results.....
Albert
On 05/11/2012 05:12 PM, Ross Walker wrote:
> Hi Tales,
>
>> I tried to leap DPPE lipid by using lipid11 force field in
>> AmberTools12,
>> but there is a problem. It splits a DPPE molecule into three parts.
> This is correct. As in the format should be 1Tail1, 1Head, 1Tail2, TER,
> 2Tail1, 2Head, 2Tail2, TER, ...
>
>> I used Charmm-GUI to get a DPPE pdb file. Then I used
>> charmmlipid2amber.x (
>> the new version in mailing list ) to convert it. It seems correct.
>>
>> *ATOM 33 C12 PA 1 ... MEMB*
>> *...*
>> *ATOM 121 H16T PA 1 ... MEMB*
>> *ATOM 1 N31 PE 1 ... MEMB*
>> *...*
>> *ATOM 32 O12 PE 1 ... MEMB*
>> *ATOM 24 C12 PA 1 ... MEMB*
>> *...*
>> *ATOM 78 H16T PA 1 ... MEMB*
>> *TER *
>> *
>> *
>> After checking the pdb file, I used tleap to get the prmtop, inpcrd and
>> new
>> pdb files.
> Yeap so this all looks good at this point.
>
>> *source leaprc.lipid11*
>> *dppe = loadpdb dppe.pdb*
>> *savepdb dppe_new.pdb*
>> *saveamberparm dppe.prmtop dppe.inpcrd*
>>
>>
>> Then I checked dppe_new.pdb, it like this:
>>
>> *ATOM 1 C116 PA 1 ...*
>> *...*
>> *ATOM 46 H2S PA 1 ...*
>> *TER*
>> *ATOM 47 C11 PE 2 ...*
>> *...*
>> *ATOM 75 O22 PE 2 ...*
>> *TER*
>> *ATOM 76 C116 PA 3 ...*
>> *...*
>> *ATOM 121 H2S PA 3 ...*
>> *TER*
>>
>> A dppe molecule was splited to three residues. So how can I get the
>> correct
>> results without the redundant "TER" ?
> This looks like a bug in the Leap code itself. Ben can you take a look at
> this and see if you reproduce the behavior please and if so file a bug
> report for Leap.
>
> What happens if you use ptraj to make your pdb file instead of leap?
>
> I.e.
>
> trajin dppe.inpcrd
> trajout dppe_new.pdb pdb
>
> Does this still put the TER cards in between the residues within the three
> residues making up a lipid unit?
>
> For the moment if that doesn't work the solution, I am afraid, is to go
> through and manually remove all the excess TER cards. It shouldn't be too
> hard to script though, you basically need a loop that removes the first 2
> out of every three TER cards in the file. Then you should be able to use
> this again in Leap - I assume so that you can insert a protein in the lipid
> file yes? - Otherwise why are you reading the pdb file back in?
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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Received on Fri May 11 2012 - 09:00:02 PDT
