I would advise you to be careful when removing parts of an experimental structure (even if only hydrogens). Although you may be fine, there are things that can go wrong (e.g. protonation states) depending on how accurate is your experimental structure and how you add the missing parts later....
As for the errors you are getting, looks to me that you have some issues in your starting structure that need to be discussed with somebody more experienced before running lots of simulations to avoid that later your calculations will be skewed. TER cards mark the end of a chain. If you have multiple subunits/domains you need to add these cards in between them. If residues are missing, homology modelling might be what you need (as Tom said). But then, homology modeling maybe tricky if the missing parts have anything to do with the function of your protein
Bottomline, things may be more complicated and just running blindly over the setup procedure without a detailed understanding of your structure may give you problems later. As Tom said, do a a careful visual analysis of your structure before attempting building the topology to identify problems ...More, read carefully the original article describing the experimental structure to identify potential incompleteness (the article and also the beader of the PDB should tell you which parts are missing).
If you don't have anybody more experienced at your institution and will still be struggling, I can offer to look over your structure on Monday (if you send it on my email address).
Best
Vlad
On March 12, 2016 7:07:45 AM GMT+01:00, Sreemol G <sreemolinfo.gmail.com> wrote:
>I have used "pdb4amber -i rnacomplex.pdb -o new.pdb --nohyd --dry" this
>command to remove hydrogens. I got a notice "gap of 5.280009 A between
>VAL_162 and PHE_163
>You MUST (!!!) insert a TER record between the residues listed above
>and
>consider to introduce caps (ACE and NME) at the dangling N- and
>C-terminals". So, I have added TER statement in the PDB file between
>VAL
>162 and PHE 163 residues now I can able to generate prmtop and inpcrd
>files. can you please tell me why it is asking to add TER statement and
>what it is doing???
>
>
>On Fri, Mar 11, 2016 at 7:19 PM, David A Case <david.case.rutgers.edu>
>wrote:
>
>> On Fri, Mar 11, 2016, Sreemol G wrote:
>>
>> > Actually i have tried but i'm getting errors when i try to save my
>> topology
>> > and coordinate files.I have used the forcefield "leaprc.ff14SB"
>when i
>> > loaded pdb i got the message and when i tried to save the topology
>file
>> and
>> > coordinate file i'm getting following error
>> > Created a new atom named: HT1 within residue: .R<NGLY 18>
>> > Created a new atom named: HT2 within residue: .R<NGLY 18>
>> > Created a new atom named: HT3 within residue: .R<NGLY 18>
>> > Created a new atom named: HN within residue: .R<ARG 19>
>>
>> ...etc
>>
>> To expand on what Vlad said, your input PDB has very non-standard
>atom
>> names
>> (where did it come from?). Simplest approach (which Amber users
>should use
>> much more often!) is to use pdb4amber with the "--nohyd" option to
>remove
>> hydrogens. See the manual, or just type "pdb4amber --help" to get
>more
>> info.
>>
>> ...dac
>>
>>
>> _______________________________________________
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>>
>
>
>
>--
>With kind regards,
>G. Sreemol
>M.Tech (Computational Biology)
>Anna university
>Chennai.
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>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
--
Sent from my Android device with K-9 Mail. Please excuse my brevity.
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Received on Fri Mar 11 2016 - 23:00:05 PST
