VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Mar 21 2011 - 19:42:50 CDT

Hi Francesco,
Why are you surprised that a *gaff* topology doesn't match *charmm* atom
names and types?

Did you try building your molecule with psfgen as I suggested? If you
did, and you still have an extra atom, what is it?

Peter

On 03/21/2011 12:50 PM, Francesco Pietra wrote:
> Hi Peter:
> I have checked all bonds, angles, and dihedrals in the .rtf topology
> file created with antechamber-charmmgen. They are correct. However,
> the .rtf list below has no correspondence in top_all27_ prot_lipid.rtf
> (which I used for the protein and the lipidic membrane) and seem to be
> related to the lower-case usage - without dots - in GAFF ff of
> antechamber. Could that be at the origin of the mess?
>
> *********************************
> * Topology File.
> *
> 99 1
> MASS 1 ca 12.010000
> MASS 2 c3 12.010000
> MASS 3 ha 1.008000
> MASS 4 hc 1.008000
> MASS 5 c 12.010000
> MASS 6 o 16.000000
> MASS 7 oh 16.000000
> MASS 8 ho 1.008000
>
> RESI RIB 0.002
> GROUP
> ATOM C ca -0.097300
> ATOM C1 ca -0.112000
> ATOM C2 ca -0.130000
> ATOM C3 ca -0.065300
> ATOM C4 ca -0.130000
> ATOM C5 ca -0.112000
> ATOM C6 c3 -0.038100
> ATOM C7 c3 -0.063700
> ATOM C8 c3 -0.092100
> ATOM C9 c3 -0.092100
> ATOM C10 c3 -0.053400
> ATOM H ha 0.134000
> ATOM H4 ha 0.135000
> ATOM H5 ha 0.135000
> ATOM H6 ha 0.148000
> ATOM H7 hc 0.049700
> ATOM H8 hc 0.050700
> ATOM H9 hc 0.031700
> ATOM H10 hc 0.039700
> ATOM H11 hc 0.034700
> ATOM H12 hc 0.032700
> ATOM H13 hc 0.034700
> ATOM H14 hc 0.036700
> ATOM H15 hc 0.051700
> ATOM C11 c 0.639100
> ATOM O o -0.548000
> ATOM O1 oh -0.608100
> ATOM H16 ho 0.443000
> ATOM C12 c3 -0.089100
> ATOM H17 hc 0.085700
> ATOM H1 hc 0.043700
> ATOM H2 hc 0.050700
> ATOM H3 hc 0.056700
>
>
> here
>
> ca: aromatic C
>
> c3: ali C
>
> ha: H at aromatic C
>
> hc: H at ali C
>
> c: carbonyl C
>
> o: carbonyl O
>
> oh: oxygen of -OH
>
> ho: H of -OH
> ******************************
>
> Thanks a lot for opinions about
>
> francesco
>
> On Mon, Mar 21, 2011 at 11:48 AM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>> Hi Francesco,
>> The key question is, are the CHARMMGEN .inp/.rtf files correct? Either
>> they are wrong, or one of the assumptions that autopsf makes is invalid
>> for that structure and you need to change your settings. The best way to
>> check is to (a) manually inspect the .inp/.rtf files and make sure that
>> the atoms and connectivity match your expectations, and (b) try
>> generating the ibuprofen using psfgen instead of autopsf so that you
>> have finer control over what is being done to the molecule.
>>
>> Best,
>> Peter
>>
>> On 03/21/2011 06:12 AM, Francesco Pietra wrote:
>>> Hi:
>>> I wonder whether there is experience with coming to AUTOPSF with
>>> .inp/.rtf files generated for non-protein organic molecules with the
>>> AMBER10's tool CHARMMGEN. The web is silent to this concern.
>>>
>>> I am in trouble with ANTECHAMBER-CHARMMGEN for complex non-proteic
>>> ligands. Thererore, I tried with a simple ligand, ibuprofen. Using .ac
>>> type files (not .mol2 which caused immediately troubles to CHARMMGEN)
>>> from ANTECHAMBER, CHARMMGEN generated .inp/.rtf files that were
>>> accepted as topology by AUTOPSF, getting .psf/.pdb. AUTOPSF counted 34
>>> atoms, which I corrected to 33, as they are. However, loading these
>>> files to VMD, bond connections appear heavily altered. No more
>>> ibuprofen.
>>>
>>> Uncertain whether problems arising from my skipping PARATOOL (I am no
>>> GAUSSIAN owner) can be posted here, to avoid overloading the mailing
>>> list, I am not attaching files here. However, I would be happy to do
>>> that if there is interest (or kindness to help)
>>>
>>> Thanks
>>>
>>> francesco pietra
>>