Hi,
I think this has already been discussed in the Archive. The problem is that sulfur is incorrectly written into parm file (?). See the -1 in:
QMMM: Atom number: 26 has atomic number -1.
Check in the Archive to be sure, but from what I remember it should be sufficient to correct this issue (the atomic number)
M.
-----Original Message-----
From: Sunanda Samanta via AMBER <amber.ambermd.org>
Sent: Monday, August 5, 2024 8:03 AM
To: amber.ambermd.org
Subject: [AMBER] No QM parameter for a Sulfur atom
[EXTERNAL EMAIL]
Dear AMBER Community,
For the QM/MM simulation of a covalently bound ligand to a Ser residue, we considered the Ser-ligand as a modified amino acid (SEN).
Following Antechamber, the atom type for a sulfur present in the ligand part was given as "SO".
ATOM 20 SAR SEN 46 -15.313 1.434 -29.065 2.849000 SO
While trying to run a QM/MM simulation, we got the following error in the output file for minimization-
3.1 QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: Atom number: 26 has atomic number -1.
QMMM: There are no PM3 parameters for this element. Sorry.
SANDER BOMB in subroutine qm2_load_params_and_allocate UNSUPPORTED ELEMENT QM PM3 NOT AVAILABLE FOR THIS ATOM
This error pertains to the sulfur atom, and its coordinates in the minimization output file were written as following -
QMMM: QM_NO. MM_NO.* ATOM* X Y Z
QMMM: 26 710 *^.^.* -1.0743 -0.8644 -2.3790
The input file for minimization contained the following, which we obtained from the AMBER tutorial for QM/MM MD (
https://ambermd.org/tutorials/advanced/tutorial2/section3.php) -
Initial min of our structure QMMM
&cntrl
imin=1, maxcyc=500, ncyc=200,
cut=8.0, ntb=1, ntc=2, ntf=2,
ifqnt=1
/
&qmmm
qmmask=':46',
qmcharge=-1,
qm_theory='PM3',
qmshake=1,
qm_ewald=1, qm_pme=1
/
I tried with some other qm_theory such as 'PM6' and 'AM1', which gave the same error. *A conventional all-atom MD*, however, *ran successfully with the same prepared files*. Is the error because of the "SO" atom type? I would be grateful for any guidance on this topic. On another note, is running a QM/MM simulation on a GPU using *pmemd.CUDA *possible? Is there any way for faster calculation than sander?
Thank You
Sincerely,
Sunanda Samanta
MSCPh.D.
BSBE, IIT Indore
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato e-mailová zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její přílohy v žádném ohledu Univerzitu Karlovu k ničemu nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní odpovědnost Univerzity Karlovy. Obsahuje-li tento e-mail nebo některá z jeho příloh osobní údaje, dbejte při jeho dalším zpracování (zejména při archivaci) souladu s pravidly evropského nařízení GDPR.
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 Charles University. 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 Charles University. If this e-mail or any of its attachments contains personal data, please be aware of data processing (particularly document management and archival policy) in accordance with Regulation (EU) 2016/679 of the European Parliament and of the Council on GDPR.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 05 2024 - 01:30:01 PDT
