Dwight
Thank you, much appreciated.
I did as you suggested.
The total charge of my COMPLEX is 2.000
I added Cl- (addions COMPLEX Cl- 0) and solvated the box.
When I tried to save the parameter file, I got
For atom: .R<Cl- 127>.A<Cl- 1> Could not find type: Cl-
For atom: .R<Cl- 128>.A<Cl- 1> Could not find type: Cl-
Parameter file was not saved.
Looking at leaprc.constph I see that atom Type Cl- is defined.
Any suggestions for this.
Best regards
George
On Jun 14, 2012, at 6:43 PM, Dwight McGee wrote:
> Hi,
>
> The error was printed because you were using the wrong force field. You
> should load *leaprc.constph* instead for Constant pH simulations.
>
> On Thu, Jun 14, 2012 at 11:52 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> I am trying to generate a topology file for a low pH MD simulation.
>>
>> I renamed the HIS, GLU and ASP residues in the starting PDB file to HIP,
>> GL4, AS4.
>>
>> For tleap I'm using leaprc.ff99SB
>>
>> Loading my protein.pdb file I get, for example,
>>
>> Unknown residue: AS4 number: 5 type: Nonterminal
>> etc.
>>
>> Trying to save the topology file, generates FATAL errors of the type
>>
>> FATAL: Atom .R<AS4 7>.A<N 1> does not have a type.
>>
>> I checked the mail archive and couldn't find anything that could help me
>> solve this problem.
>>
>> Your help will be appreciated
>>
>> Best regards
>>
>> George
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>>
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> Graduate Student
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
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Received on Thu Jun 14 2012 - 12:30:02 PDT
