[gmx-users] adding an acid as n-terminus
jalemkul at vt.edu
Thu Nov 13 19:33:40 CET 2014
On 11/13/14 6:07 AM, Mark Abraham wrote:
> On Thu, Nov 13, 2014 at 11:45 AM, Velia Minicozzi <
> velia.minicozzi at roma2.infn.it> wrote:
>> Dear gmx-users,
>> we want to simulate a peptide which starts with an acidic terminus.
>> We used PRODRG to compute the coordinates and the FF for this new
>> residue and we followed all the gromacs instructions to insert a new
>> residue (http://www.gromacs.org/Documentation/How-tos/Adding_
>> Following the instructions, we inserted the new residue in the
>> gromos43a1ff rtp file and
>> we changed the hdb file accordingly.
>> Pdb2gmx give us the following error that we do not understand.
>> What else should we change?
> You want to get pdb2gmx to build your polypeptide, so the topology you got
> from PRODRG must be modified so that it follows the .rtp format, and has
> the right + or - indicators to show where the bonds to other residues will
> form. You haven't showed your work there, so we're left guessing
>> We add to the email the pdbfile and the itp file computed by PRODRG
The charges from PRODRG are highly suspicious. I suggest manual
reparametrization. PRODRG topologies generally lead to serious artifacts.
>> pdb2gmx -f provapept2.pdb -o provapept2.gro -p topol2.top -ignh -ter
>> Fatal error:
>> Residue 2 named ACI of a molecule in the input file was mapped
>> to an entry in the topology database, but the atom C used in
>> that entry is not found in the input file. Perhaps your atom
>> and/or residue naming needs to be fixed.
> This means what it says. pdb2gmx recognized in your .pdb file an ACl
> residue that it found in your .rtp database, but the .pdb file had no atom
> named C. Whether it should depends on things you haven't told us.
>> Velia Minicozzi
>> Universita' di Roma Tor Vergata
>> Dipartimento di Fisica
>> via della Ricerca Scientifica 1, I-00133 ROMA, Italy
>> Tel. +39.06.7259.4440 Fax +39.06.2023.507
>> Email: minicozzi at roma2.infn.it
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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