From: Francesco Pietra (
Date: Mon Mar 21 2011 - 11:50:13 CDT

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
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


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


On Mon, Mar 21, 2011 at 11:48 AM, Peter Freddolino <> 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