Hi Zahra,
I experienced similar problems. Just renaming atom CL to to Cl in your
pdb file should do the trick. Before antechamber, I always treat my
ligand pdb file with this command:
sed -i 's/ CL/ Cl/g' %s/lig_ini.pdb
best regards,
Juraj
On 16. 03. 21 8:23, Aliakbartehrani Zahra wrote:
> Dear all,
> I have faced an issue in tleap for preparation of. top and .rst files for my protein-ligand complex. There are 2 chlorine atoms in ligand structure, and I have used GAFF for the ligand atom. I have used .prep, .lib and .frcmod files for ligand but there is still problem:
> FATAL: Atom .R<SDF 369>.A<CL72 72> does not have a type.
> FATAL: Atom .R<SDF 369>.A<CL82 73> does not have a type.
> Any help will be appreciated.
> Bests
> Zahra
> I have used these commands for running antechamber and tleap:
> in antechamber:
> antechamber -i lig-WithH.pdb -fi pdb -nc 0 -o lig-WithH.mol2 -fo mol2 -c bcc -s 2
> parmchk2 -i lig-WithH.mol2 -f mol2 -o lig-WithH.frcmod
> in tleap:
> source leaprc.ff99SB
> source leaprc.gaff
> source leaprc.water.tip3p
> set default pbradii mbondi2
> loadAmberParams frcmod.ionsjc_tip3p
> loadmol2 lig-WithH.mol2
> loadamberprep lig-WithH.prep
> loadamberparams lig-WithH.frcmod
> loadoff lig-WithH.lib
> complex = loadpdb lig-complex.pdb
> solvatebox complex TIP3PBOX 15.0 2.00
> addions complex Na+ 8
> saveamberparm complex lig-complex.top lig-complex.rst
> savepdb complex lig-complex-tleap.pdb
> quit
>
> -----
>
> Upozornení: Není-li v této zpráve výslovne uvedeno jinak, má tato e-mailová zpráva nebo její prílohy pouze informativní charakter. Tato zpráva ani její prílohy v zádném ohledu Biotechnologický ústav AV CR, v. v. i. k nicemu nezavazují. Text této zprávy nebo jejích príloh není návrhem na uzavrení smlouvy, ani prijetím prípadného návrhu na uzavrení smlouvy, ani jiným právním jednáním smerujícím k uzavrení jakékoliv smlouvy a nezakládá predsmluvní odpovednost Biotechnologického ústavu AV CR, v. v. i.
>
> Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institute of Biotechnology of the Czech Academy of Sciences. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, nor the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract, nor does it create any pre-contractual liability on the part of Institute of Biotechnology of the Czech Academy of Sciences.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 16 2021 - 01:30:03 PDT
