Re: [gmx-users] OPLS-AA Unknown Atomtype

2011-08-29 Thread Yao Yao
in the ffoplsaabon.itp.  Is there any other file I also need to mention those values? Thanks, Yao From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, August 23, 2011 2:07 PM Subject: Re: [gmx-users] OPLS-AA

Re: [gmx-users] OPLS-AA Unknown Atomtype

2011-08-29 Thread Justin A. Lemkul
Yao Yao wrote: Hi Justin, Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp, but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like, Back Off! I just backed up mdout.mdp to

Re: [gmx-users] OPLS-AA Unknown Atomtype

2011-08-29 Thread Yao Yao
to modify. Thanks, yao From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, August 29, 2011 3:41 AM Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype Yao Yao wrote: Hi Justin, Thanks for your

Re: [gmx-users] OPLS-AA Unknown Atomtype

2011-08-29 Thread Justin A. Lemkul
*From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Monday, August 29, 2011 3:41 AM *Subject:* Re: [gmx-users] OPLS-AA Unknown Atomtype Yao Yao wrote: Hi Justin, Thanks for your last reply. Now it seems that OPLS has

[gmx-users] OPLS-AA Unknown Atomtype

2011-08-23 Thread Yao Yao
Hi all, I am constructing a new molecule in OPLS force field. Though I modified ffbonded.itp, ffnonbonded.itp, atomtypes.atp aminoacids.rtp, it still gives error Unknown Molecule_Atomtype. I have opened all the files in the OPLS force field but really do not see any other files I could modify.

Re: [gmx-users] OPLS-AA Unknown Atomtype

2011-08-23 Thread Justin A. Lemkul
Yao Yao wrote: Hi all, I am constructing a new molecule in OPLS force field. Though I modified ffbonded.itp, ffnonbonded.itp, atomtypes.atp aminoacids.rtp, it still gives error Unknown Molecule_Atomtype. I have opened all the files in the OPLS force field but really do not see any other

Re: [gmx-users] OPLS-AA Unknown Atomtype

2011-08-23 Thread Justin A. Lemkul
Yao Yao wrote: Hi Justin, Thanks for your reply. Here is the exact error message, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file