Hi all
Thanks for your valuable comments. In fact there was problem with my
input file as there was TER card added in my pdb.
I have tried to modify the script and generated correct input pdb file.
I have complex system (membrane+protein) converted from coarse grain
simulation to all atoms, and therefore naming scheme for lipid atoms was
completely different than what is mentioned in the charmmlipid2amber.x
script. So we had written python script to convert atom names as given
in charmmlipid2amber.x but did not maintained the order of tail1,tail2
and head groups i-e PA-PC-OL.
I am trying now with seemingly correct POPC lipid molecule order, i hope
this time it will work. I have tried with correct POPC and DOPC membrane
system and all is well.
But as i am using membrane-protein i hope i wont have surface tension
issue with lipid14, as also mentioned by Callum J.Dickson.
with best regards
Mustafa
On 03/20/2014 07:13 PM, Benjamin Madej wrote:
> Hi Mustafa,
>
> Yes, it sounds like the prmtop/inpcrd did not correctly link the lipid
> "residues" together into a lipid molecule.
>
> Verify that you are sourcing your force field files correctly, and read the
> leap.log file carefully. It also could be an issue with the residue and
> atom naming and TER card format in your input file. Double-check that your
> PDB file follows the Lipid11/Lipid14 format as described in the AmberTools
> manual and the Lipid11 paper.
>
> The warnings about "name change in pdb file residue" are normal and to be
> expected if you're using the charmmlipid2amber.x script to format your
> input PDB.
>
> It also appears that the residue and molecule types are not being found in
> the name map. Can you confirm that you are correctly sourcing the
> leaprc.lipid14 and leaprc.ff12SB files?
>
> When you say "there is TER flag introduced by tleap", how did you generate
> a PDB? The only way that I know of that correctly inserts TER cards for the
> conversion of Lipid11/Lipid14 prmtop/inpcrd to PDBs is the program
> "ambpdb". See the AmberTools manual for more details about ambpdb. If in a
> PDB generated by ambpdb, you see TER cards after each residue, then the
> connectivity is wrong.
>
> If all of that doesn't work, we'll need more information about your input
> PDB file format as well as the leap.log file to diagnose your problem.
>
> Finally, I strongly recommend that you use Amber for the actual production
> of your system. Lipid14 is fully compatible with GPU accelerated Amber and
> we ran all of our validation calculations with GPU accelerated Amber13.
>
> All the best,
> Ben Madej
> Walker Molecular Dynamics Lab
>
>
> On Thu, Mar 20, 2014 at 8:50 AM, Ghulam Mustafa <ghulam.mustafa.h-its.org>wrote:
>
>> Dear All
>>
>> I am trying to use new amber lipid14 ff on my protein-membrane complex
>> system but i get strange results after running heating and equilibration
>> (1.5ns) step. The head group of POPC lipid molecules fall apart from the
>> tails and keep floating in water box above and below the z axes of
>> bilayer. I have run initial minimization using Amber and then switching
>> to NAMD using amber forcefields (ff12SB and LIPID14).
>>
>> Although i find some warning in tleap while loading lipid-protein
>> complex but i can successfully prepare coordinate and topology files.
>> These warnings are as below:
>>
>> Enter zPdbReadScan from call depth 0.
>> Warning: name change in pdb file residue 492 ;
>> this residue is split into OL and PC.
>> Warning: name change in pdb file residue 492 ;
>> this residue is split into PC and PA.
>> Warning: name change in pdb file residue 493 ;
>> this residue is split into OL and PC.
>> Warning: name change in pdb file residue 493 ;
>> this residue is split into PC and PA.
>> Warning: name change in pdb file residue 494 ;
>> so on ..........
>> and for proteins:
>>
>> (Residue 1: ASP, Nonterminal, was not found in name map.)
>> (Residue 2: SER, Nonterminal, was not found in name map.)
>> (Residue 3: LEU, Nonterminal, was not found in name map.)
>> (Residue 4: VAL, Nonterminal, was not found in name map.)
>> (Residue 5: VAL, Nonterminal, was not found in name map.)
>> (Residue 6: LEU, Nonterminal, was not found in name map.)
>> (Residue 7: VAL, Nonterminal, was not found in name map.)
>>
>> similarly for ions
>>
>> (Residue 881: Na+, Nonterminal, was not found in name map.)
>> (Residue 882: Cl-, Nonterminal, was not found in name map.)
>> (Residue 883: Cl-, Nonterminal, was not found in name map.)
>> (Residue 884: Cl-, Nonterminal, was not found in name map.)
>> (Residue 885: Na+, Nonterminal, was not found in name map.)
>> (Residue 886: Na+, Nonterminal, was not found in name map.)
>> (Residue 887: Na+, Nonterminal, was not found in name map.)
>> (Residue 888: Na+, Nonterminal, was not found in name map.)
>> (Residue 889: Na+, Nonterminal, was not found in name map.)
>>
>> for solvent
>>
>> (Residue 1461: WAT, Nonterminal, was not found in name map.)
>> (Residue 1462: WAT, Nonterminal, was not found in name map.)
>> (Residue 1463: WAT, Nonterminal, was not found in name map.)
>> (Residue 1464: WAT, Nonterminal, was not found in name map.)
>> (Residue 1465: WAT, Nonterminal, was not found in name map.)
>> (Residue 1466: WAT, Nonterminal, was not found in name map.)
>> (Residue 1467: WAT, Nonterminal, was not found in name map.)
>> (Residue 1468: WAT, Nonterminal, was not found in name map.)
>> (Residue 1469: WAT, Nonterminal, was not found in name map.)
>> (Residue 1470: WAT, Nonterminal, was not found in name map.)
>>
>> and for lipids :
>>
>> (Residue 79964: PC, Terminal/last, was not found in name map.)
>> (Residue 79965: PA, Terminal/last, was not found in name map.)
>> (Residue 79966: OL, Terminal/last, was not found in name map.)
>> (Residue 79967: PC, Terminal/last, was not found in name map.)
>> (Residue 79968: PA, Terminal/last, was not found in name map.)
>> (Residue 79969: OL, Terminal/last, was not found in name map.)
>> (Residue 79970: PC, Terminal/last, was not found in name map.)
>> (Residue 79971: PA, Terminal/last, was not found in name map.)
>> (Residue 79972: OL, Terminal/last, was not found in name map.)
>> (Residue 79973: PC, Terminal/last, was not found in name map.)
>> (Residue 79974: PA, Terminal/last, was not found in name map.)
>> (Residue 79975: OL, Terminal/last, was not found in name map.)
>> (Residue 79976: PC, Terminal/last, was not found in name map.)
>> (Residue 79977: PA, Terminal/last, was not found in name map.)
>>
>> Is there something wrong with my initial coordinate and topology files?
>> as it seems there is no connectivity between head and tail groups, and
>> also there is TER flag introduced by tleap between each tail, head and
>> tail molecules.
>>
>> Looking for your kind input in this regard
>>
>> Mustafa
>>
>>
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Received on Fri Mar 21 2014 - 10:00:02 PDT
